Starting phenix.real_space_refine on Sun May 12 16:42:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v6l_42995/05_2024/8v6l_42995_updated.pdb" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 136 5.16 5 Na 3 4.78 5 C 14724 2.51 5 N 3552 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 22387 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "C" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5315 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 634} Chain breaks: 1 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 283 Unusual residues: {' NA': 2, 'I8E': 1, 'POV': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 334 Unusual residues: {' NA': 1, 'I8E': 1, 'POV': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 281 Unusual residues: {'I8E': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 229 Unusual residues: {'I8E': 1, 'POV': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 11.41, per 1000 atoms: 0.51 Number of scatterers: 22387 At special positions: 0 Unit cell: (136.95, 136.95, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 20 15.00 Na 3 11.00 O 3952 8.00 N 3552 7.00 C 14724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.57 Conformation dependent library (CDL) restraints added in 4.3 seconds 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 0 sheets defined 55.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.886A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.516A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.558A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 438 through 457 Processing helix chain 'A' and resid 480 through 507 removed outlier: 3.819A pdb=" N LEU A 484 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 485 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET A 488 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 490 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 499 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.962A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 567 removed outlier: 4.244A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 4.114A pdb=" N MET A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR A 575 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE A 579 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 608 removed outlier: 4.340A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.805A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.890A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 removed outlier: 4.516A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 299 through 306 removed outlier: 3.576A pdb=" N VAL B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 354 through 361 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 438 through 457 Processing helix chain 'B' and resid 480 through 507 removed outlier: 3.813A pdb=" N LEU B 484 " --> pdb=" O TRP B 481 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 485 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG B 487 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET B 488 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 490 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 492 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 499 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 513 No H-bonds generated for 'chain 'B' and resid 510 through 513' Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.956A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 567 removed outlier: 4.242A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR B 565 " --> pdb=" O ASN B 561 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 575 through 585 removed outlier: 4.104A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 4.344A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'B' and resid 652 through 665 Processing helix chain 'B' and resid 670 through 686 removed outlier: 3.872A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.890A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 removed outlier: 4.519A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 283 Processing helix chain 'C' and resid 299 through 306 removed outlier: 3.560A pdb=" N VAL C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 435 Processing helix chain 'C' and resid 438 through 457 Processing helix chain 'C' and resid 480 through 507 removed outlier: 3.817A pdb=" N LEU C 484 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 485 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG C 487 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET C 488 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 490 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE C 492 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 494 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 499 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU C 501 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 513 No H-bonds generated for 'chain 'C' and resid 510 through 513' Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.968A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 567 removed outlier: 4.243A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ARG C 567 " --> pdb=" O LEU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 575 through 581 removed outlier: 4.022A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 608 removed outlier: 4.345A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 625 through 637 Processing helix chain 'C' and resid 652 through 665 Processing helix chain 'C' and resid 670 through 686 removed outlier: 3.831A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.889A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 161 removed outlier: 4.511A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 283 Processing helix chain 'D' and resid 299 through 306 removed outlier: 3.553A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 328 Processing helix chain 'D' and resid 333 through 335 No H-bonds generated for 'chain 'D' and resid 333 through 335' Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'D' and resid 354 through 361 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 425 through 435 Processing helix chain 'D' and resid 438 through 457 Processing helix chain 'D' and resid 480 through 507 removed outlier: 3.819A pdb=" N LEU D 484 " --> pdb=" O TRP D 481 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU D 485 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG D 487 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET D 488 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE D 489 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL D 490 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 492 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 494 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 499 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU D 501 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 513 No H-bonds generated for 'chain 'D' and resid 510 through 513' Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.969A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 567 removed outlier: 4.245A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TYR D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR D 565 " --> pdb=" O ASN D 561 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ARG D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 573 No H-bonds generated for 'chain 'D' and resid 571 through 573' Processing helix chain 'D' and resid 575 through 583 removed outlier: 4.021A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 608 removed outlier: 4.341A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 597 " --> pdb=" O VAL D 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 652 through 665 Processing helix chain 'D' and resid 670 through 686 removed outlier: 3.827A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 739 through 749 841 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.64 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3787 1.33 - 1.45: 5727 1.45 - 1.57: 13062 1.57 - 1.70: 40 1.70 - 1.82: 224 Bond restraints: 22840 Sorted by residual: bond pdb=" O12 POV C 903 " pdb=" P POV C 903 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.57e+00 bond pdb=" O12 POV B 901 " pdb=" P POV B 901 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" O12 POV B 907 " pdb=" P POV B 907 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O12 POV D 903 " pdb=" P POV D 903 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.45e+00 ... (remaining 22835 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.94: 288 104.94 - 112.21: 11288 112.21 - 119.48: 7997 119.48 - 126.75: 10836 126.75 - 134.01: 303 Bond angle restraints: 30712 Sorted by residual: angle pdb=" N ARG D 462 " pdb=" CA ARG D 462 " pdb=" C ARG D 462 " ideal model delta sigma weight residual 109.42 104.30 5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N CYS A 619 " pdb=" CA CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sigma weight residual 114.17 110.51 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N CYS C 619 " pdb=" CA CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sigma weight residual 114.17 110.53 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" N CYS B 619 " pdb=" CA CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sigma weight residual 114.17 110.60 3.57 1.14e+00 7.69e-01 9.79e+00 angle pdb=" N ARG C 462 " pdb=" CA ARG C 462 " pdb=" C ARG C 462 " ideal model delta sigma weight residual 109.44 104.45 4.99 1.81e+00 3.05e-01 7.60e+00 ... (remaining 30707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 13653 34.83 - 69.66: 290 69.66 - 104.50: 40 104.50 - 139.33: 12 139.33 - 174.16: 17 Dihedral angle restraints: 14012 sinusoidal: 6308 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR D 461 " pdb=" C TYR D 461 " pdb=" N ARG D 462 " pdb=" CA ARG D 462 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N ARG B 462 " pdb=" CA ARG B 462 " ideal model delta harmonic sigma weight residual 180.00 152.40 27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TYR A 461 " pdb=" C TYR A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 14009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2483 0.035 - 0.071: 694 0.071 - 0.106: 160 0.106 - 0.142: 24 0.142 - 0.177: 11 Chirality restraints: 3372 Sorted by residual: chirality pdb=" C2 POV C 904 " pdb=" C1 POV C 904 " pdb=" C3 POV C 904 " pdb=" O21 POV C 904 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C2 POV C 902 " pdb=" C1 POV C 902 " pdb=" C3 POV C 902 " pdb=" O21 POV C 902 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" C2 POV B 903 " pdb=" C1 POV B 903 " pdb=" C3 POV B 903 " pdb=" O21 POV B 903 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 3369 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 I8E B 906 " -0.012 2.00e-02 2.50e+03 2.60e-02 1.68e+01 pdb=" C17 I8E B 906 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E B 906 " 0.024 2.00e-02 2.50e+03 pdb=" C4 I8E B 906 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E B 906 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E B 906 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E B 906 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E B 906 " -0.019 2.00e-02 2.50e+03 pdb=" O15 I8E B 906 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E B 906 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E D 905 " 0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E D 905 " 0.017 2.00e-02 2.50e+03 pdb=" C3 I8E D 905 " -0.023 2.00e-02 2.50e+03 pdb=" C4 I8E D 905 " 0.016 2.00e-02 2.50e+03 pdb=" C5 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" C6 I8E D 905 " 0.013 2.00e-02 2.50e+03 pdb=" C7 I8E D 905 " 0.018 2.00e-02 2.50e+03 pdb=" C8 I8E D 905 " 0.020 2.00e-02 2.50e+03 pdb=" O15 I8E D 905 " -0.045 2.00e-02 2.50e+03 pdb=" O21 I8E D 905 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 I8E C 905 " -0.012 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" C17 I8E C 905 " -0.017 2.00e-02 2.50e+03 pdb=" C3 I8E C 905 " 0.023 2.00e-02 2.50e+03 pdb=" C4 I8E C 905 " -0.016 2.00e-02 2.50e+03 pdb=" C5 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" C6 I8E C 905 " -0.013 2.00e-02 2.50e+03 pdb=" C7 I8E C 905 " -0.018 2.00e-02 2.50e+03 pdb=" C8 I8E C 905 " -0.020 2.00e-02 2.50e+03 pdb=" O15 I8E C 905 " 0.045 2.00e-02 2.50e+03 pdb=" O21 I8E C 905 " 0.047 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 213 2.58 - 3.16: 20417 3.16 - 3.74: 32413 3.74 - 4.32: 44004 4.32 - 4.90: 74531 Nonbonded interactions: 171578 Sorted by model distance: nonbonded pdb=" OG SER C 624 " pdb=" O13 POV C 904 " model vdw 2.001 2.440 nonbonded pdb=" OG SER B 624 " pdb=" O13 POV B 905 " model vdw 2.005 2.440 nonbonded pdb=" OG SER D 624 " pdb=" O13 POV D 904 " model vdw 2.009 2.440 nonbonded pdb=" OG SER A 444 " pdb=" O13 POV A 902 " model vdw 2.155 2.440 nonbonded pdb=" OG SER D 444 " pdb=" O13 POV D 903 " model vdw 2.161 2.440 ... (remaining 171573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'B' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'C' and (resid 59 through 751 or resid 901 through 903)) selection = (chain 'D' and (resid 59 through 751 or resid 901 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.670 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.250 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22840 Z= 0.277 Angle : 0.628 5.344 30712 Z= 0.319 Chirality : 0.036 0.177 3372 Planarity : 0.004 0.082 3736 Dihedral : 16.488 174.158 8980 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 5.12 % Allowed : 9.47 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.18), residues: 2596 helix: 0.88 (0.14), residues: 1552 sheet: -3.17 (0.59), residues: 64 loop : -3.52 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 521 HIS 0.006 0.001 HIS C 471 PHE 0.009 0.001 PHE B 316 TYR 0.013 0.001 TYR D 451 ARG 0.003 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 533 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.9010 (m) cc_final: 0.8779 (p) REVERT: A 347 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8026 (tt) REVERT: A 483 GLN cc_start: 0.7044 (tp40) cc_final: 0.6489 (tm-30) REVERT: A 485 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7653 (tm) REVERT: A 650 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5601 (m-10) REVERT: A 661 TYR cc_start: 0.8735 (t80) cc_final: 0.8337 (t80) REVERT: A 663 ILE cc_start: 0.9132 (tt) cc_final: 0.8914 (mt) REVERT: B 121 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8647 (mmmt) REVERT: B 336 THR cc_start: 0.9019 (m) cc_final: 0.8762 (p) REVERT: B 347 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 358 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (tptt) REVERT: B 483 GLN cc_start: 0.6919 (tp40) cc_final: 0.6400 (tm-30) REVERT: B 485 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7660 (tm) REVERT: B 650 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: B 661 TYR cc_start: 0.8738 (t80) cc_final: 0.8359 (t80) REVERT: B 663 ILE cc_start: 0.9144 (tt) cc_final: 0.8897 (mt) REVERT: C 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8658 (mmmt) REVERT: C 336 THR cc_start: 0.9015 (m) cc_final: 0.8753 (p) REVERT: C 347 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7939 (tt) REVERT: C 358 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8631 (tptt) REVERT: C 483 GLN cc_start: 0.7030 (tp40) cc_final: 0.6431 (tm-30) REVERT: C 485 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7645 (tm) REVERT: C 650 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5615 (m-10) REVERT: C 661 TYR cc_start: 0.8744 (t80) cc_final: 0.8354 (t80) REVERT: C 663 ILE cc_start: 0.9120 (tt) cc_final: 0.8875 (mt) REVERT: D 121 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8657 (mmmt) REVERT: D 336 THR cc_start: 0.9019 (m) cc_final: 0.8757 (p) REVERT: D 347 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7953 (tt) REVERT: D 358 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8642 (tptt) REVERT: D 483 GLN cc_start: 0.7032 (tp40) cc_final: 0.6420 (tm-30) REVERT: D 485 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7686 (tm) REVERT: D 650 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: D 661 TYR cc_start: 0.8760 (t80) cc_final: 0.8371 (t80) REVERT: D 663 ILE cc_start: 0.9153 (tt) cc_final: 0.8934 (mt) outliers start: 119 outliers final: 43 residues processed: 652 average time/residue: 0.3956 time to fit residues: 382.7732 Evaluate side-chains 371 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 313 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 227 GLN A 274 GLN A 346 GLN A 417 HIS ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 227 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 417 HIS ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 274 GLN C 346 GLN C 417 HIS ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 227 GLN D 274 GLN D 346 GLN D 417 HIS ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22840 Z= 0.390 Angle : 0.780 10.131 30712 Z= 0.379 Chirality : 0.044 0.181 3372 Planarity : 0.005 0.076 3736 Dihedral : 19.066 179.070 3938 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 6.28 % Allowed : 16.52 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2596 helix: 0.59 (0.14), residues: 1560 sheet: -2.72 (0.67), residues: 40 loop : -3.35 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 521 HIS 0.005 0.001 HIS D 471 PHE 0.022 0.002 PHE A 590 TYR 0.021 0.002 TYR D 461 ARG 0.005 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 347 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8309 (mtpt) REVERT: A 166 ASP cc_start: 0.7971 (t70) cc_final: 0.7657 (t0) REVERT: A 281 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 322 ASP cc_start: 0.8262 (t70) cc_final: 0.8057 (t70) REVERT: A 429 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 483 GLN cc_start: 0.6900 (tp40) cc_final: 0.6632 (tm-30) REVERT: A 485 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7380 (tm) REVERT: A 548 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 631 GLU cc_start: 0.8377 (tp30) cc_final: 0.8030 (tp30) REVERT: A 641 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7616 (p0) REVERT: A 650 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5849 (m-10) REVERT: B 121 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8410 (mtpt) REVERT: B 166 ASP cc_start: 0.8096 (t70) cc_final: 0.7662 (t0) REVERT: B 281 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7883 (mm) REVERT: B 322 ASP cc_start: 0.8378 (t70) cc_final: 0.8165 (t70) REVERT: B 358 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8839 (tttp) REVERT: B 429 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 483 GLN cc_start: 0.6902 (tp40) cc_final: 0.6562 (tm-30) REVERT: B 485 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7479 (tm) REVERT: B 548 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7548 (mt) REVERT: B 619 CYS cc_start: 0.1135 (OUTLIER) cc_final: 0.0799 (t) REVERT: B 641 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7510 (p0) REVERT: B 650 TYR cc_start: 0.6266 (OUTLIER) cc_final: 0.5900 (m-10) REVERT: C 166 ASP cc_start: 0.8104 (t70) cc_final: 0.7765 (t0) REVERT: C 281 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7889 (mm) REVERT: C 322 ASP cc_start: 0.8365 (t70) cc_final: 0.8150 (t70) REVERT: C 358 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8844 (tttp) REVERT: C 429 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7721 (mp) REVERT: C 483 GLN cc_start: 0.6884 (tp40) cc_final: 0.6574 (tm-30) REVERT: C 485 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7462 (tm) REVERT: C 548 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7551 (mt) REVERT: C 619 CYS cc_start: 0.1193 (OUTLIER) cc_final: 0.0893 (t) REVERT: C 641 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7553 (p0) REVERT: C 650 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5818 (m-10) REVERT: D 121 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8622 (mmmt) REVERT: D 166 ASP cc_start: 0.8091 (t70) cc_final: 0.7656 (t0) REVERT: D 281 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7878 (mm) REVERT: D 322 ASP cc_start: 0.8349 (t70) cc_final: 0.8140 (t70) REVERT: D 358 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8846 (tttp) REVERT: D 429 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7740 (mp) REVERT: D 483 GLN cc_start: 0.6885 (tp40) cc_final: 0.6624 (tm-30) REVERT: D 485 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7481 (tm) REVERT: D 619 CYS cc_start: 0.0963 (OUTLIER) cc_final: 0.0745 (t) REVERT: D 641 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7473 (p0) REVERT: D 650 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5834 (m-10) outliers start: 146 outliers final: 86 residues processed: 467 average time/residue: 0.3264 time to fit residues: 240.1904 Evaluate side-chains 411 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 296 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 619 CYS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 9.9990 chunk 255 optimal weight: 0.8980 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 160 HIS B 274 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22840 Z= 0.321 Angle : 0.720 7.788 30712 Z= 0.354 Chirality : 0.042 0.172 3372 Planarity : 0.004 0.074 3736 Dihedral : 18.510 176.899 3926 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.87 % Favored : 86.98 % Rotamer: Outliers : 8.39 % Allowed : 16.91 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2596 helix: 0.48 (0.13), residues: 1572 sheet: -2.04 (0.71), residues: 40 loop : -3.36 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 692 HIS 0.005 0.001 HIS B 471 PHE 0.017 0.001 PHE A 590 TYR 0.014 0.002 TYR D 451 ARG 0.007 0.001 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 337 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8265 (mtpt) REVERT: A 166 ASP cc_start: 0.7982 (t70) cc_final: 0.7597 (t0) REVERT: A 255 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8348 (mt0) REVERT: A 268 LEU cc_start: 0.9429 (tm) cc_final: 0.9154 (tt) REVERT: A 429 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7801 (mp) REVERT: A 483 GLN cc_start: 0.6986 (tp40) cc_final: 0.6688 (tm-30) REVERT: A 485 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7297 (tm) REVERT: A 637 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5786 (pt) REVERT: A 641 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7817 (p0) REVERT: A 650 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.5712 (m-10) REVERT: B 121 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8359 (mtpt) REVERT: B 166 ASP cc_start: 0.8107 (t70) cc_final: 0.7692 (t0) REVERT: B 268 LEU cc_start: 0.9417 (tm) cc_final: 0.9184 (tt) REVERT: B 322 ASP cc_start: 0.8357 (t70) cc_final: 0.8141 (t70) REVERT: B 358 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8841 (tttp) REVERT: B 429 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7707 (mp) REVERT: B 483 GLN cc_start: 0.7028 (tp40) cc_final: 0.6647 (tm-30) REVERT: B 637 ILE cc_start: 0.6130 (OUTLIER) cc_final: 0.5780 (pt) REVERT: B 641 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7776 (p0) REVERT: B 650 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: C 166 ASP cc_start: 0.8111 (t70) cc_final: 0.7688 (t0) REVERT: C 255 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8334 (mt0) REVERT: C 268 LEU cc_start: 0.9411 (tm) cc_final: 0.9165 (tt) REVERT: C 322 ASP cc_start: 0.8347 (t70) cc_final: 0.8127 (t70) REVERT: C 336 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8725 (p) REVERT: C 358 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8848 (tttp) REVERT: C 429 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7678 (mp) REVERT: C 483 GLN cc_start: 0.7055 (tp40) cc_final: 0.6690 (tm-30) REVERT: C 578 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7856 (mmp) REVERT: C 637 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5807 (pt) REVERT: C 641 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7722 (p0) REVERT: C 650 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5775 (m-10) REVERT: D 119 LEU cc_start: 0.8339 (mm) cc_final: 0.8115 (mm) REVERT: D 121 LYS cc_start: 0.8821 (mmtp) cc_final: 0.8390 (mtpt) REVERT: D 255 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8322 (mt0) REVERT: D 268 LEU cc_start: 0.9393 (tm) cc_final: 0.9162 (tt) REVERT: D 358 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8862 (tttp) REVERT: D 429 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7702 (mp) REVERT: D 460 TYR cc_start: 0.7554 (t80) cc_final: 0.7283 (t80) REVERT: D 483 GLN cc_start: 0.7015 (tp40) cc_final: 0.6674 (tm-30) REVERT: D 637 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5846 (pt) REVERT: D 641 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7735 (p0) REVERT: D 650 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5798 (m-10) outliers start: 195 outliers final: 117 residues processed: 493 average time/residue: 0.3275 time to fit residues: 255.5635 Evaluate side-chains 445 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 306 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22840 Z= 0.251 Angle : 0.686 8.460 30712 Z= 0.336 Chirality : 0.040 0.161 3372 Planarity : 0.004 0.073 3736 Dihedral : 17.880 179.687 3920 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.75 % Favored : 87.13 % Rotamer: Outliers : 7.83 % Allowed : 18.16 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2596 helix: 0.51 (0.13), residues: 1572 sheet: -1.73 (0.73), residues: 40 loop : -3.31 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 493 HIS 0.005 0.001 HIS A 471 PHE 0.014 0.001 PHE D 316 TYR 0.012 0.001 TYR D 451 ARG 0.006 0.000 ARG D 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 330 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8272 (mtpt) REVERT: A 166 ASP cc_start: 0.7956 (t70) cc_final: 0.7590 (t0) REVERT: A 255 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8325 (mt0) REVERT: A 429 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 483 GLN cc_start: 0.7038 (tp40) cc_final: 0.6722 (tm-30) REVERT: A 637 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5644 (pt) REVERT: A 650 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5570 (m-10) REVERT: B 121 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8281 (mtpt) REVERT: B 166 ASP cc_start: 0.8089 (t70) cc_final: 0.7686 (t0) REVERT: B 322 ASP cc_start: 0.8344 (t70) cc_final: 0.8106 (t70) REVERT: B 358 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8809 (tttp) REVERT: B 429 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 483 GLN cc_start: 0.7125 (tp40) cc_final: 0.6737 (tm-30) REVERT: B 586 ASP cc_start: 0.8915 (m-30) cc_final: 0.8608 (t0) REVERT: B 637 ILE cc_start: 0.5994 (OUTLIER) cc_final: 0.5671 (pt) REVERT: B 641 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7833 (p0) REVERT: B 650 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5778 (m-10) REVERT: C 166 ASP cc_start: 0.8147 (t70) cc_final: 0.7737 (t0) REVERT: C 322 ASP cc_start: 0.8334 (t70) cc_final: 0.8111 (t70) REVERT: C 358 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8810 (tttp) REVERT: C 429 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7623 (mp) REVERT: C 483 GLN cc_start: 0.7031 (tp40) cc_final: 0.6713 (tm-30) REVERT: C 637 ILE cc_start: 0.6011 (OUTLIER) cc_final: 0.5687 (pt) REVERT: C 641 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7792 (p0) REVERT: C 650 TYR cc_start: 0.6246 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: D 119 LEU cc_start: 0.8346 (mm) cc_final: 0.8096 (mm) REVERT: D 121 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8302 (mtpt) REVERT: D 255 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8310 (mt0) REVERT: D 358 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8810 (tttp) REVERT: D 429 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7640 (mp) REVERT: D 460 TYR cc_start: 0.7583 (t80) cc_final: 0.7319 (t80) REVERT: D 483 GLN cc_start: 0.7024 (tp40) cc_final: 0.6719 (tm-30) REVERT: D 637 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5693 (pt) REVERT: D 641 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7784 (p0) REVERT: D 650 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5810 (m-10) outliers start: 182 outliers final: 122 residues processed: 486 average time/residue: 0.3300 time to fit residues: 251.5930 Evaluate side-chains 448 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 308 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 242 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 242 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 22840 Z= 0.496 Angle : 0.819 8.274 30712 Z= 0.403 Chirality : 0.045 0.186 3372 Planarity : 0.005 0.070 3736 Dihedral : 17.488 166.371 3920 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.98 % Favored : 85.98 % Rotamer: Outliers : 7.92 % Allowed : 19.88 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.17), residues: 2596 helix: 0.24 (0.13), residues: 1572 sheet: -2.12 (0.73), residues: 40 loop : -3.45 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 493 HIS 0.005 0.001 HIS D 417 PHE 0.023 0.002 PHE D 590 TYR 0.017 0.002 TYR D 451 ARG 0.005 0.001 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 308 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8283 (mtpt) REVERT: A 166 ASP cc_start: 0.8018 (t70) cc_final: 0.7689 (t0) REVERT: A 429 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 483 GLN cc_start: 0.7189 (tp40) cc_final: 0.6404 (tm-30) REVERT: A 485 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.6989 (tm) REVERT: A 637 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6498 (pt) REVERT: A 641 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 650 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: B 121 LYS cc_start: 0.8759 (mmtp) cc_final: 0.8243 (mtpt) REVERT: B 166 ASP cc_start: 0.8133 (t70) cc_final: 0.7760 (t0) REVERT: B 358 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8764 (tttp) REVERT: B 429 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7628 (mp) REVERT: B 483 GLN cc_start: 0.7091 (tp40) cc_final: 0.6379 (tm-30) REVERT: B 586 ASP cc_start: 0.8878 (m-30) cc_final: 0.8595 (t0) REVERT: B 637 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6485 (pt) REVERT: B 641 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7782 (p0) REVERT: B 649 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7290 (mptt) REVERT: B 650 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.5880 (m-10) REVERT: C 121 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8333 (mtpt) REVERT: C 358 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8762 (tttp) REVERT: C 429 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 483 GLN cc_start: 0.7135 (tp40) cc_final: 0.6398 (tm-30) REVERT: C 637 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6462 (pt) REVERT: C 641 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7733 (p0) REVERT: C 650 TYR cc_start: 0.6411 (OUTLIER) cc_final: 0.5923 (m-10) REVERT: D 119 LEU cc_start: 0.8343 (mm) cc_final: 0.8131 (mm) REVERT: D 121 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8350 (mtpt) REVERT: D 358 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8627 (tptt) REVERT: D 429 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7632 (mp) REVERT: D 483 GLN cc_start: 0.7125 (tp40) cc_final: 0.6426 (tm-30) REVERT: D 637 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6513 (pt) REVERT: D 641 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7752 (p0) REVERT: D 650 TYR cc_start: 0.6373 (OUTLIER) cc_final: 0.5856 (m-10) outliers start: 184 outliers final: 134 residues processed: 474 average time/residue: 0.3366 time to fit residues: 248.6590 Evaluate side-chains 444 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 290 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 452 ASN Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 641 ASP Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 734 ILE Chi-restraints excluded: chain D residue 746 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 251 optimal weight: 0.3980 chunk 208 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22840 Z= 0.172 Angle : 0.674 9.379 30712 Z= 0.332 Chirality : 0.040 0.195 3372 Planarity : 0.004 0.073 3736 Dihedral : 16.652 162.267 3914 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.75 % Favored : 88.17 % Rotamer: Outliers : 6.11 % Allowed : 21.99 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2596 helix: 0.55 (0.14), residues: 1564 sheet: -1.87 (0.77), residues: 40 loop : -3.31 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 493 HIS 0.011 0.001 HIS C 585 PHE 0.014 0.001 PHE B 316 TYR 0.015 0.001 TYR C 540 ARG 0.005 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 338 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8234 (mtpt) REVERT: A 166 ASP cc_start: 0.7983 (t70) cc_final: 0.7620 (t0) REVERT: A 429 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7718 (mp) REVERT: A 578 MET cc_start: 0.8131 (mmp) cc_final: 0.7636 (mmp) REVERT: A 637 ILE cc_start: 0.5907 (OUTLIER) cc_final: 0.5516 (pt) REVERT: A 650 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.5547 (m-10) REVERT: B 121 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8215 (mtpt) REVERT: B 166 ASP cc_start: 0.8111 (t70) cc_final: 0.7730 (t0) REVERT: B 255 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8315 (mt0) REVERT: B 358 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8613 (tptt) REVERT: B 429 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7513 (mp) REVERT: B 586 ASP cc_start: 0.8816 (m-30) cc_final: 0.8485 (t0) REVERT: B 637 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5551 (pt) REVERT: B 650 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5659 (m-10) REVERT: C 121 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8223 (mtpt) REVERT: C 255 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8330 (mt0) REVERT: C 358 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8600 (tptt) REVERT: C 429 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7522 (mp) REVERT: C 637 ILE cc_start: 0.5899 (OUTLIER) cc_final: 0.5531 (pt) REVERT: C 650 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5537 (m-10) REVERT: D 119 LEU cc_start: 0.8224 (mm) cc_final: 0.7994 (mm) REVERT: D 121 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8251 (mtpt) REVERT: D 358 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8591 (tptt) REVERT: D 429 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7532 (mp) REVERT: D 460 TYR cc_start: 0.7513 (t80) cc_final: 0.7263 (t80) REVERT: D 618 ASP cc_start: 0.6328 (OUTLIER) cc_final: 0.4760 (m-30) REVERT: D 637 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5632 (pt) REVERT: D 650 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5508 (m-10) outliers start: 142 outliers final: 90 residues processed: 465 average time/residue: 0.3306 time to fit residues: 242.7086 Evaluate side-chains 409 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 303 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22840 Z= 0.321 Angle : 0.708 7.563 30712 Z= 0.351 Chirality : 0.042 0.157 3372 Planarity : 0.004 0.071 3736 Dihedral : 16.432 159.222 3914 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 6.54 % Allowed : 22.46 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2596 helix: 0.46 (0.14), residues: 1560 sheet: -2.30 (0.76), residues: 40 loop : -3.39 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 493 HIS 0.004 0.001 HIS C 417 PHE 0.019 0.001 PHE D 316 TYR 0.017 0.002 TYR A 540 ARG 0.004 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 287 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8232 (mtpt) REVERT: A 429 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 479 MET cc_start: 0.3170 (tpp) cc_final: 0.2683 (tpp) REVERT: A 586 ASP cc_start: 0.8912 (m-30) cc_final: 0.8538 (t0) REVERT: A 637 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.5957 (pt) REVERT: A 650 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5470 (m-10) REVERT: B 121 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8204 (mtpt) REVERT: B 166 ASP cc_start: 0.8136 (t70) cc_final: 0.7778 (t0) REVERT: B 358 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8622 (tptt) REVERT: B 429 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 637 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.5958 (pt) REVERT: B 650 TYR cc_start: 0.6147 (OUTLIER) cc_final: 0.5720 (m-10) REVERT: C 121 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8206 (mtpt) REVERT: C 358 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8620 (tptt) REVERT: C 429 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7559 (mp) REVERT: C 637 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5997 (pt) REVERT: C 650 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5565 (m-10) REVERT: D 119 LEU cc_start: 0.8265 (mm) cc_final: 0.8041 (mm) REVERT: D 121 LYS cc_start: 0.8769 (mmtp) cc_final: 0.8245 (mtpt) REVERT: D 358 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8608 (tptt) REVERT: D 429 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7588 (mp) REVERT: D 637 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6066 (pt) REVERT: D 650 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5454 (m-10) outliers start: 152 outliers final: 116 residues processed: 421 average time/residue: 0.3391 time to fit residues: 226.9198 Evaluate side-chains 404 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 273 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 464 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22840 Z= 0.317 Angle : 0.744 17.569 30712 Z= 0.361 Chirality : 0.042 0.178 3372 Planarity : 0.004 0.072 3736 Dihedral : 16.269 156.946 3914 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.52 % Favored : 86.33 % Rotamer: Outliers : 6.11 % Allowed : 23.02 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2596 helix: 0.44 (0.14), residues: 1556 sheet: -2.60 (0.78), residues: 40 loop : -3.47 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 493 HIS 0.008 0.001 HIS C 585 PHE 0.020 0.001 PHE D 316 TYR 0.012 0.002 TYR C 208 ARG 0.004 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 280 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8173 (mtpt) REVERT: A 429 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 479 MET cc_start: 0.2994 (tpp) cc_final: 0.2396 (tpp) REVERT: A 586 ASP cc_start: 0.8896 (m-30) cc_final: 0.8536 (t0) REVERT: A 637 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5923 (pt) REVERT: A 650 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5508 (m-10) REVERT: B 121 LYS cc_start: 0.8745 (mmtp) cc_final: 0.8196 (mtpt) REVERT: B 166 ASP cc_start: 0.8132 (t70) cc_final: 0.7778 (t0) REVERT: B 358 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8635 (tptt) REVERT: B 429 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7643 (mp) REVERT: B 586 ASP cc_start: 0.8951 (m-30) cc_final: 0.8636 (t0) REVERT: B 619 CYS cc_start: -0.0393 (OUTLIER) cc_final: -0.1382 (t) REVERT: B 637 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.6027 (pt) REVERT: B 650 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5689 (m-10) REVERT: B 725 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: C 121 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8162 (mtpt) REVERT: C 255 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8396 (mt0) REVERT: C 358 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8596 (tptt) REVERT: C 429 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7576 (mp) REVERT: C 637 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6026 (pt) REVERT: C 650 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5534 (m-10) REVERT: D 119 LEU cc_start: 0.8255 (mm) cc_final: 0.8030 (mm) REVERT: D 121 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8277 (mtpt) REVERT: D 358 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8627 (tptt) REVERT: D 429 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7598 (mp) REVERT: D 637 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6101 (pt) REVERT: D 650 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5418 (m-10) outliers start: 142 outliers final: 110 residues processed: 403 average time/residue: 0.3403 time to fit residues: 214.6047 Evaluate side-chains 397 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 270 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 254 TYR Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 646 GLN Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 219 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22840 Z= 0.263 Angle : 0.717 16.391 30712 Z= 0.350 Chirality : 0.041 0.170 3372 Planarity : 0.004 0.070 3736 Dihedral : 16.048 155.254 3914 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.41 % Favored : 86.48 % Rotamer: Outliers : 5.72 % Allowed : 23.32 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2596 helix: 0.49 (0.14), residues: 1552 sheet: -2.73 (0.78), residues: 40 loop : -3.48 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 493 HIS 0.004 0.001 HIS C 417 PHE 0.019 0.001 PHE B 316 TYR 0.010 0.001 TYR D 451 ARG 0.003 0.000 ARG C 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 283 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8173 (mtpt) REVERT: A 429 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7572 (mp) REVERT: A 479 MET cc_start: 0.2865 (tpp) cc_final: 0.2244 (tpp) REVERT: A 586 ASP cc_start: 0.8866 (m-30) cc_final: 0.8517 (t0) REVERT: A 637 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.5959 (pt) REVERT: A 650 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5468 (m-10) REVERT: B 121 LYS cc_start: 0.8734 (mmtp) cc_final: 0.8185 (mtpt) REVERT: B 166 ASP cc_start: 0.8134 (t70) cc_final: 0.7791 (t0) REVERT: B 358 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8605 (tptt) REVERT: B 429 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 586 ASP cc_start: 0.8943 (m-30) cc_final: 0.8602 (t0) REVERT: B 637 ILE cc_start: 0.6309 (OUTLIER) cc_final: 0.5963 (pt) REVERT: B 650 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5624 (m-10) REVERT: B 725 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: C 121 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8131 (mtpt) REVERT: C 358 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8591 (tptt) REVERT: C 429 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7442 (mp) REVERT: C 618 ASP cc_start: 0.5819 (OUTLIER) cc_final: 0.4345 (m-30) REVERT: C 637 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.5938 (pt) REVERT: C 650 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5459 (m-10) REVERT: D 119 LEU cc_start: 0.8243 (mm) cc_final: 0.8007 (mm) REVERT: D 121 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8266 (mtpt) REVERT: D 358 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8623 (tptt) REVERT: D 429 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7478 (mp) REVERT: D 637 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.5968 (pt) REVERT: D 650 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5445 (m-10) REVERT: D 717 MET cc_start: 0.7526 (mtp) cc_final: 0.7315 (mtt) outliers start: 133 outliers final: 106 residues processed: 395 average time/residue: 0.3222 time to fit residues: 201.6302 Evaluate side-chains 398 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 275 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 646 GLN Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 9.9990 chunk 246 optimal weight: 0.0370 chunk 150 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 22840 Z= 0.276 Angle : 0.884 59.181 30712 Z= 0.474 Chirality : 0.041 0.318 3372 Planarity : 0.005 0.164 3736 Dihedral : 16.042 155.294 3914 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.48 % Favored : 86.40 % Rotamer: Outliers : 5.55 % Allowed : 23.49 % Favored : 70.96 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2596 helix: 0.52 (0.14), residues: 1552 sheet: -2.74 (0.78), residues: 40 loop : -3.47 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 493 HIS 0.019 0.001 HIS A 417 PHE 0.019 0.001 PHE C 316 TYR 0.010 0.001 TYR B 661 ARG 0.019 0.000 ARG A 690 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5192 Ramachandran restraints generated. 2596 Oldfield, 0 Emsley, 2596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 275 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8173 (mtpt) REVERT: A 429 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 479 MET cc_start: 0.2838 (tpp) cc_final: 0.2241 (tpp) REVERT: A 586 ASP cc_start: 0.8850 (m-30) cc_final: 0.8509 (t0) REVERT: A 637 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.5940 (pt) REVERT: A 650 TYR cc_start: 0.6112 (OUTLIER) cc_final: 0.5456 (m-10) REVERT: B 121 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8183 (mtpt) REVERT: B 166 ASP cc_start: 0.8174 (t70) cc_final: 0.7820 (t0) REVERT: B 358 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8605 (tptt) REVERT: B 429 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7625 (mp) REVERT: B 586 ASP cc_start: 0.8936 (m-30) cc_final: 0.8598 (t0) REVERT: B 637 ILE cc_start: 0.6316 (OUTLIER) cc_final: 0.5965 (pt) REVERT: B 650 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5610 (m-10) REVERT: B 725 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: C 121 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8128 (mtpt) REVERT: C 358 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8538 (tptt) REVERT: C 429 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7438 (mp) REVERT: C 618 ASP cc_start: 0.5856 (OUTLIER) cc_final: 0.4369 (m-30) REVERT: C 637 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5921 (pt) REVERT: C 650 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: D 119 LEU cc_start: 0.8238 (mm) cc_final: 0.8006 (mm) REVERT: D 121 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8264 (mtpt) REVERT: D 358 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8621 (tptt) REVERT: D 429 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7456 (mp) REVERT: D 586 ASP cc_start: 0.8929 (m-30) cc_final: 0.8568 (t0) REVERT: D 637 ILE cc_start: 0.6352 (OUTLIER) cc_final: 0.5986 (pt) REVERT: D 650 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5440 (m-10) outliers start: 129 outliers final: 110 residues processed: 384 average time/residue: 0.3178 time to fit residues: 195.0404 Evaluate side-chains 400 residues out of total 2324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 273 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 464 ARG Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 430 HIS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 650 TYR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 734 ILE Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 298 ASN Chi-restraints excluded: chain C residue 316 PHE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 618 ASP Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 646 GLN Chi-restraints excluded: chain C residue 650 TYR Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 668 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 316 PHE Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 LYS Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 650 TYR Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain D residue 657 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 668 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 734 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 0.0040 chunk 86 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.162788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123622 restraints weight = 30159.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127413 restraints weight = 21965.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129231 restraints weight = 17549.793| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 22840 Z= 0.275 Angle : 0.884 59.200 30712 Z= 0.474 Chirality : 0.041 0.318 3372 Planarity : 0.005 0.164 3736 Dihedral : 16.042 155.294 3914 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.48 % Favored : 86.40 % Rotamer: Outliers : 5.51 % Allowed : 23.49 % Favored : 71.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2596 helix: 0.52 (0.14), residues: 1552 sheet: -2.74 (0.78), residues: 40 loop : -3.47 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 493 HIS 0.019 0.001 HIS A 417 PHE 0.019 0.001 PHE C 316 TYR 0.010 0.001 TYR B 661 ARG 0.019 0.000 ARG A 690 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4750.36 seconds wall clock time: 87 minutes 47.61 seconds (5267.61 seconds total)