Starting phenix.real_space_refine on Sat Feb 17 23:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2t_23140/02_2024/7l2t_23140_updated.pdb" } resolution = 3.08 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= 0.000 sd= 0.007 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 8 5.49 5 S 134 5.16 5 Na 1 4.78 5 C 13140 2.51 5 N 3235 2.21 5 O 3649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20167 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4662 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 562} Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4657 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 4653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4653 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 561} Chain: "D" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4720 Classifications: {'peptide': 584} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 568} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' NA': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'65I': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'65I': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'65I': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.75, per 1000 atoms: 0.53 Number of scatterers: 20167 At special positions: 0 Unit cell: (129.018, 127.32, 130.715, 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 134 16.00 P 8 15.00 Na 1 11.00 O 3649 8.00 N 3235 7.00 C 13140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.04 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " 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: 7.56 Conformation dependent library (CDL) restraints added in 3.4 seconds 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 8 sheets defined 53.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 157 through 163 Processing helix chain 'A' and resid 171 through 183 Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 4.205A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 416 through 428 removed outlier: 4.040A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 508 No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 3.625A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.756A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 3.851A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 684 removed outlier: 3.607A pdb=" N MET A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 removed outlier: 4.779A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TRP A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 171 through 183 Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.999A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.808A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 536 through 556 removed outlier: 3.601A pdb=" N SER B 540 " --> pdb=" O TYR B 537 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.878A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.938A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 680 Processing helix chain 'B' and resid 689 through 710 removed outlier: 3.648A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 187 through 190 No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 268 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 4.197A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.320A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 505 through 508 No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.605A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 577 through 598 removed outlier: 3.756A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.855A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 683 removed outlier: 3.699A pdb=" N MET C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY C 683 " --> pdb=" O ILE C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 710 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 157 through 163 Processing helix chain 'D' and resid 171 through 183 Processing helix chain 'D' and resid 187 through 190 No H-bonds generated for 'chain 'D' and resid 187 through 190' Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 214 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 4.409A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.880A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.902A pdb=" N PHE D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.745A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.180A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG D 579 " --> pdb=" O ARG D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 4.009A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 684 removed outlier: 3.750A pdb=" N MET D 682 " --> pdb=" O LEU D 678 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 711 removed outlier: 3.509A pdb=" N ASN D 695 " --> pdb=" O GLN D 691 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 741 through 747 removed outlier: 3.519A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= C, first strand: chain 'F' and resid 61 through 63 Processing sheet with id= D, first strand: chain 'E' and resid 21 through 23 Processing sheet with id= E, first strand: chain 'E' and resid 61 through 63 Processing sheet with id= F, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.629A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.530A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.550A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 902 hydrogen bonds defined for protein. 2511 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: 5.80 Time building geometry restraints manager: 8.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3147 1.31 - 1.44: 5770 1.44 - 1.56: 11485 1.56 - 1.69: 16 1.69 - 1.82: 204 Bond restraints: 20622 Sorted by residual: bond pdb=" C11 65I E 902 " pdb=" O6 65I E 902 " ideal model delta sigma weight residual 1.331 1.408 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C11 65I F 901 " pdb=" O6 65I F 901 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C11 65I E 901 " pdb=" O6 65I E 901 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C11 65I B 802 " pdb=" O6 65I B 802 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C5 65I B 802 " pdb=" O1 65I B 802 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.04e+01 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 428 106.83 - 113.64: 11169 113.64 - 120.44: 8502 120.44 - 127.25: 7603 127.25 - 134.06: 177 Bond angle restraints: 27879 Sorted by residual: angle pdb=" N ARG A 721 " pdb=" CA ARG A 721 " pdb=" C ARG A 721 " ideal model delta sigma weight residual 108.78 119.37 -10.59 8.20e-01 1.49e+00 1.67e+02 angle pdb=" N SER A 722 " pdb=" CA SER A 722 " pdb=" C SER A 722 " ideal model delta sigma weight residual 112.87 121.75 -8.88 1.20e+00 6.94e-01 5.48e+01 angle pdb=" N SER C 722 " pdb=" CA SER C 722 " pdb=" C SER C 722 " ideal model delta sigma weight residual 112.38 120.89 -8.51 1.22e+00 6.72e-01 4.86e+01 angle pdb=" N VAL D 728 " pdb=" CA VAL D 728 " pdb=" C VAL D 728 " ideal model delta sigma weight residual 111.62 107.53 4.09 7.90e-01 1.60e+00 2.68e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 ... (remaining 27874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 12133 34.29 - 68.57: 131 68.57 - 102.86: 35 102.86 - 137.15: 6 137.15 - 171.44: 4 Dihedral angle restraints: 12309 sinusoidal: 5063 harmonic: 7246 Sorted by residual: dihedral pdb=" CA VAL D 415 " pdb=" C VAL D 415 " pdb=" N GLU D 416 " pdb=" CA GLU D 416 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PHE A 712 " pdb=" C PHE A 712 " pdb=" N LEU A 713 " pdb=" CA LEU A 713 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C16 XJ7 B 801 " pdb=" C17 XJ7 B 801 " pdb=" C18 XJ7 B 801 " pdb=" C19 XJ7 B 801 " ideal model delta sinusoidal sigma weight residual 141.98 -46.58 -171.44 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 12306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 3121 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.027: 0 4.027 - 5.033: 8 Chirality restraints: 3129 Sorted by residual: chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C3 XJ7 C 801 " pdb=" C2 XJ7 C 801 " pdb=" C24 XJ7 C 801 " pdb=" O3 XJ7 C 801 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.50 -5.00 2.00e-01 2.50e+01 6.26e+02 ... (remaining 3126 not shown) Planarity restraints: 3446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 694 " -0.021 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" C LYS A 694 " 0.071 2.00e-02 2.50e+03 pdb=" O LYS A 694 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN A 695 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 544 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C SER C 544 " 0.040 2.00e-02 2.50e+03 pdb=" O SER C 544 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU C 545 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 543 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C PHE C 543 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE C 543 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 544 " 0.013 2.00e-02 2.50e+03 ... (remaining 3443 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6791 2.86 - 3.37: 19184 3.37 - 3.88: 31581 3.88 - 4.39: 35829 4.39 - 4.90: 62765 Nonbonded interactions: 156150 Sorted by model distance: nonbonded pdb=" OD2 ASP C 178 " pdb=" NZ LYS C 182 " model vdw 2.348 2.520 nonbonded pdb=" OD1 ASP B 509 " pdb=" N SER B 510 " model vdw 2.365 2.520 nonbonded pdb=" OD2 ASP B 509 " pdb=" O XJ7 B 801 " model vdw 2.376 2.440 nonbonded pdb=" OE2 GLU B 210 " pdb=" OH TYR C 374 " model vdw 2.389 2.440 nonbonded pdb=" OD1 ASP A 509 " pdb=" N SER A 510 " model vdw 2.393 2.520 ... (remaining 156145 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 153 through 238 or resid 242 through 751 or resid 801)) selection = (chain 'B' and (resid 153 through 751 or resid 801)) selection = (chain 'C' and (resid 153 through 238 or resid 242 through 751 or resid 801)) selection = (chain 'D' and (resid 153 through 238 or resid 242 through 751 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 1 through 75 or resid 901)) selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.590 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 51.550 Find NCS groups from input model: 1.720 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: 0.000 Load rotamer database and sin/cos tables:3.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.077 20622 Z= 0.252 Angle : 0.717 12.528 27879 Z= 0.381 Chirality : 0.256 5.033 3129 Planarity : 0.004 0.041 3446 Dihedral : 12.978 171.435 7614 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.60 % Allowed : 1.15 % Favored : 98.25 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.71 % 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: 0.70 (0.17), residues: 2449 helix: 1.79 (0.14), residues: 1349 sheet: -0.14 (0.55), residues: 76 loop : -1.36 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 549 HIS 0.002 0.001 HIS B 358 PHE 0.020 0.002 PHE B 304 TYR 0.015 0.002 TYR D 631 ARG 0.002 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 445 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 TYR cc_start: 0.8189 (t80) cc_final: 0.7970 (t80) REVERT: A 523 MET cc_start: 0.8362 (tpp) cc_final: 0.8153 (tpt) REVERT: E 17 ASP cc_start: 0.6942 (t0) cc_final: 0.6734 (t0) REVERT: E 68 ILE cc_start: 0.8253 (mm) cc_final: 0.7977 (tp) REVERT: B 496 PHE cc_start: 0.6731 (m-80) cc_final: 0.6480 (m-80) REVERT: B 679 ILE cc_start: 0.6336 (mm) cc_final: 0.6088 (tp) REVERT: B 684 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5609 (pt0) REVERT: C 445 MET cc_start: 0.9019 (mmm) cc_final: 0.8524 (mmp) REVERT: C 644 MET cc_start: 0.7664 (mtp) cc_final: 0.7149 (mmm) REVERT: C 727 GLN cc_start: 0.7874 (tp40) cc_final: 0.7176 (tp40) REVERT: D 343 SER cc_start: 0.8977 (m) cc_final: 0.8744 (m) REVERT: D 523 MET cc_start: 0.8338 (tpp) cc_final: 0.8038 (tpt) outliers start: 13 outliers final: 2 residues processed: 453 average time/residue: 0.3578 time to fit residues: 237.9876 Evaluate side-chains 303 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 678 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 0.0470 chunk 98 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 220 optimal weight: 0.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN E 59 HIS B 687 ASN C 260 GLN C 393 ASN C 498 GLN C 676 ASN C 687 ASN D 393 ASN D 498 GLN D 652 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20622 Z= 0.180 Angle : 0.561 10.742 27879 Z= 0.289 Chirality : 0.044 0.436 3129 Planarity : 0.004 0.045 3446 Dihedral : 13.199 169.071 2941 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.20 % Allowed : 5.66 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.83 (0.17), residues: 2449 helix: 1.95 (0.14), residues: 1359 sheet: 0.03 (0.56), residues: 76 loop : -1.43 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 740 HIS 0.005 0.001 HIS E 59 PHE 0.016 0.001 PHE A 304 TYR 0.013 0.001 TYR D 631 ARG 0.006 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 312 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8884 (mtm) cc_final: 0.8505 (mtm) REVERT: A 460 LEU cc_start: 0.7114 (mt) cc_final: 0.6896 (mt) REVERT: E 25 MET cc_start: 0.8587 (tpp) cc_final: 0.8312 (ttm) REVERT: B 496 PHE cc_start: 0.6765 (m-80) cc_final: 0.6478 (m-80) REVERT: C 162 MET cc_start: 0.7770 (tpp) cc_final: 0.7184 (tpp) REVERT: C 211 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8406 (mmt90) REVERT: C 445 MET cc_start: 0.9108 (mmm) cc_final: 0.8681 (mmp) REVERT: C 644 MET cc_start: 0.7733 (mtp) cc_final: 0.7150 (mmm) REVERT: C 727 GLN cc_start: 0.7909 (tp40) cc_final: 0.7180 (tp40) REVERT: D 306 THR cc_start: 0.8160 (m) cc_final: 0.7782 (p) REVERT: D 343 SER cc_start: 0.8921 (m) cc_final: 0.8694 (m) REVERT: D 523 MET cc_start: 0.8400 (tpp) cc_final: 0.8191 (tpt) REVERT: D 716 MET cc_start: 0.5026 (pmm) cc_final: 0.4368 (tpt) outliers start: 26 outliers final: 16 residues processed: 325 average time/residue: 0.3165 time to fit residues: 157.3094 Evaluate side-chains 297 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 281 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 0.0870 chunk 150 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 0.6980 chunk 196 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 228 GLN E 59 HIS C 223 ASN C 393 ASN D 223 ASN D 393 ASN D 691 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20622 Z= 0.205 Angle : 0.549 9.109 27879 Z= 0.288 Chirality : 0.044 0.527 3129 Planarity : 0.004 0.047 3446 Dihedral : 12.555 161.671 2939 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.66 % Allowed : 6.44 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.78 (0.17), residues: 2449 helix: 1.94 (0.14), residues: 1359 sheet: 0.05 (0.56), residues: 76 loop : -1.51 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 740 HIS 0.009 0.001 HIS E 59 PHE 0.018 0.001 PHE B 304 TYR 0.014 0.001 TYR D 631 ARG 0.007 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (t0) REVERT: A 412 MET cc_start: 0.8887 (mtm) cc_final: 0.8521 (mtm) REVERT: C 162 MET cc_start: 0.7740 (tpp) cc_final: 0.7095 (tpp) REVERT: C 445 MET cc_start: 0.9126 (mmm) cc_final: 0.8680 (mmp) REVERT: C 572 MET cc_start: 0.7496 (ttp) cc_final: 0.6843 (tpp) REVERT: C 727 GLN cc_start: 0.8004 (tp40) cc_final: 0.7300 (tp40) REVERT: D 306 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7873 (p) REVERT: D 343 SER cc_start: 0.8937 (m) cc_final: 0.8702 (m) REVERT: D 523 MET cc_start: 0.8401 (tpp) cc_final: 0.8099 (tpt) REVERT: D 716 MET cc_start: 0.5006 (pmm) cc_final: 0.3707 (mtm) outliers start: 36 outliers final: 23 residues processed: 311 average time/residue: 0.3262 time to fit residues: 154.5396 Evaluate side-chains 300 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 397 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.0000 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 63 optimal weight: 0.0270 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN F 20 ASN E 59 HIS C 393 ASN D 691 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20622 Z= 0.121 Angle : 0.492 8.272 27879 Z= 0.260 Chirality : 0.041 0.482 3129 Planarity : 0.003 0.046 3446 Dihedral : 12.056 155.485 2939 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.93 % Allowed : 6.76 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.97 (0.17), residues: 2449 helix: 2.15 (0.14), residues: 1358 sheet: 0.16 (0.56), residues: 76 loop : -1.51 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 740 HIS 0.007 0.001 HIS E 59 PHE 0.013 0.001 PHE E 27 TYR 0.013 0.001 TYR D 631 ARG 0.007 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 293 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.8352 (mmm160) REVERT: A 412 MET cc_start: 0.8897 (mtm) cc_final: 0.8563 (mtm) REVERT: F 25 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8333 (tpp) REVERT: B 213 ASN cc_start: 0.7860 (t0) cc_final: 0.7620 (t0) REVERT: C 162 MET cc_start: 0.7724 (tpp) cc_final: 0.7119 (tpp) REVERT: C 445 MET cc_start: 0.9096 (mmm) cc_final: 0.8780 (mmp) REVERT: C 572 MET cc_start: 0.7420 (ttp) cc_final: 0.6781 (tpp) REVERT: C 727 GLN cc_start: 0.7930 (tp40) cc_final: 0.7220 (tp40) REVERT: D 306 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7914 (p) REVERT: D 343 SER cc_start: 0.8867 (m) cc_final: 0.8626 (m) REVERT: D 523 MET cc_start: 0.8388 (tpp) cc_final: 0.8136 (tpt) REVERT: D 716 MET cc_start: 0.4926 (pmm) cc_final: 0.3661 (mtm) outliers start: 42 outliers final: 31 residues processed: 311 average time/residue: 0.3282 time to fit residues: 155.2391 Evaluate side-chains 300 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain E residue 59 HIS Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 0.2980 chunk 174 optimal weight: 0.4980 chunk 96 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 0.6980 chunk 210 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 HIS C 393 ASN D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20622 Z= 0.130 Angle : 0.485 7.688 27879 Z= 0.255 Chirality : 0.040 0.452 3129 Planarity : 0.004 0.047 3446 Dihedral : 11.690 149.136 2939 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.75 % Allowed : 7.82 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 1.04 (0.18), residues: 2449 helix: 2.22 (0.14), residues: 1358 sheet: 0.28 (0.56), residues: 76 loop : -1.51 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 272 HIS 0.007 0.001 HIS E 59 PHE 0.016 0.001 PHE E 27 TYR 0.012 0.001 TYR D 631 ARG 0.009 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 286 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8344 (mmm160) REVERT: A 363 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7624 (ttt-90) REVERT: A 412 MET cc_start: 0.8909 (mtm) cc_final: 0.8592 (mtm) REVERT: B 237 LYS cc_start: 0.6810 (pttt) cc_final: 0.6598 (ptpt) REVERT: C 162 MET cc_start: 0.7760 (tpp) cc_final: 0.7185 (tpp) REVERT: C 445 MET cc_start: 0.9100 (mmm) cc_final: 0.8763 (mmp) REVERT: C 572 MET cc_start: 0.7438 (ttp) cc_final: 0.6807 (tpp) REVERT: C 727 GLN cc_start: 0.7910 (tp40) cc_final: 0.7246 (tp40) REVERT: D 306 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7937 (p) REVERT: D 310 ASN cc_start: 0.7970 (t0) cc_final: 0.7685 (t0) REVERT: D 343 SER cc_start: 0.8855 (m) cc_final: 0.8622 (m) REVERT: D 523 MET cc_start: 0.8375 (tpp) cc_final: 0.8070 (tpt) REVERT: D 716 MET cc_start: 0.4899 (pmm) cc_final: 0.3735 (mtm) outliers start: 38 outliers final: 29 residues processed: 301 average time/residue: 0.3299 time to fit residues: 150.9246 Evaluate side-chains 302 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 272 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 570 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS D 410 HIS D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20622 Z= 0.348 Angle : 0.618 8.311 27879 Z= 0.321 Chirality : 0.045 0.456 3129 Planarity : 0.004 0.050 3446 Dihedral : 11.985 153.975 2939 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.16 % Allowed : 7.77 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.50 (0.17), residues: 2449 helix: 1.70 (0.14), residues: 1365 sheet: -0.00 (0.57), residues: 78 loop : -1.67 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 697 HIS 0.006 0.001 HIS B 289 PHE 0.025 0.002 PHE B 438 TYR 0.021 0.002 TYR A 453 ARG 0.009 0.001 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 284 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7683 (ttt-90) REVERT: A 412 MET cc_start: 0.8910 (mtm) cc_final: 0.8448 (mtm) REVERT: B 384 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8290 (mp) REVERT: C 162 MET cc_start: 0.7837 (tpp) cc_final: 0.7313 (tpp) REVERT: C 572 MET cc_start: 0.7494 (ttp) cc_final: 0.6775 (tpp) REVERT: D 306 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7849 (p) REVERT: D 310 ASN cc_start: 0.8015 (t0) cc_final: 0.7727 (t0) REVERT: D 343 SER cc_start: 0.8943 (m) cc_final: 0.8697 (m) REVERT: D 523 MET cc_start: 0.8419 (tpp) cc_final: 0.8208 (tpt) REVERT: D 600 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: D 716 MET cc_start: 0.4888 (pmm) cc_final: 0.3808 (mtt) outliers start: 47 outliers final: 31 residues processed: 311 average time/residue: 0.3341 time to fit residues: 157.1660 Evaluate side-chains 305 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 171 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20622 Z= 0.142 Angle : 0.500 7.441 27879 Z= 0.267 Chirality : 0.040 0.413 3129 Planarity : 0.004 0.047 3446 Dihedral : 11.334 153.860 2936 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.70 % Allowed : 8.33 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.78 (0.17), residues: 2449 helix: 2.03 (0.14), residues: 1362 sheet: 0.25 (0.57), residues: 76 loop : -1.70 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 740 HIS 0.004 0.001 HIS C 378 PHE 0.013 0.001 PHE E 27 TYR 0.013 0.001 TYR D 631 ARG 0.008 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 279 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8331 (mmm160) REVERT: A 363 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7683 (ttt-90) REVERT: A 412 MET cc_start: 0.8925 (mtm) cc_final: 0.8514 (mtm) REVERT: B 384 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 162 MET cc_start: 0.7797 (tpp) cc_final: 0.7388 (tpp) REVERT: C 326 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8218 (mm-30) REVERT: C 363 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7472 (mtp-110) REVERT: C 572 MET cc_start: 0.7434 (ttp) cc_final: 0.6840 (tpp) REVERT: D 306 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7957 (p) REVERT: D 310 ASN cc_start: 0.7919 (t0) cc_final: 0.7666 (t0) REVERT: D 343 SER cc_start: 0.8790 (m) cc_final: 0.8568 (m) REVERT: D 523 MET cc_start: 0.8363 (tpp) cc_final: 0.8124 (tpt) REVERT: D 716 MET cc_start: 0.4800 (pmm) cc_final: 0.3555 (mtm) outliers start: 37 outliers final: 28 residues processed: 297 average time/residue: 0.3227 time to fit residues: 145.5156 Evaluate side-chains 298 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 268 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN D 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20622 Z= 0.283 Angle : 0.576 7.452 27879 Z= 0.301 Chirality : 0.043 0.429 3129 Planarity : 0.004 0.050 3446 Dihedral : 11.256 158.167 2936 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.02 % Allowed : 8.23 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.53 (0.17), residues: 2449 helix: 1.78 (0.14), residues: 1367 sheet: 0.18 (0.58), residues: 76 loop : -1.75 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 697 HIS 0.005 0.001 HIS B 289 PHE 0.022 0.002 PHE A 304 TYR 0.018 0.002 TYR A 453 ARG 0.007 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 275 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7712 (ttt-90) REVERT: A 412 MET cc_start: 0.8904 (mtm) cc_final: 0.8470 (mtm) REVERT: B 384 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8297 (mp) REVERT: B 684 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5509 (pt0) REVERT: C 162 MET cc_start: 0.7870 (tpp) cc_final: 0.7424 (tpp) REVERT: C 326 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8232 (mm-30) REVERT: C 572 MET cc_start: 0.7525 (ttp) cc_final: 0.6861 (tpp) REVERT: C 678 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7411 (tt) REVERT: D 306 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7924 (p) REVERT: D 310 ASN cc_start: 0.7960 (t0) cc_final: 0.7707 (t0) REVERT: D 343 SER cc_start: 0.8876 (m) cc_final: 0.8639 (m) REVERT: D 716 MET cc_start: 0.4785 (pmm) cc_final: 0.3378 (mtm) outliers start: 44 outliers final: 32 residues processed: 299 average time/residue: 0.3636 time to fit residues: 162.6829 Evaluate side-chains 312 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 654 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 197 optimal weight: 0.0970 chunk 206 optimal weight: 0.9980 chunk 217 optimal weight: 0.0040 chunk 143 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 ASN D 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20622 Z= 0.124 Angle : 0.491 7.285 27879 Z= 0.260 Chirality : 0.040 0.397 3129 Planarity : 0.004 0.048 3446 Dihedral : 10.762 156.999 2936 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.66 % Allowed : 8.51 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.85 (0.18), residues: 2449 helix: 2.13 (0.14), residues: 1360 sheet: 0.21 (0.58), residues: 76 loop : -1.72 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 740 HIS 0.003 0.001 HIS C 378 PHE 0.011 0.001 PHE A 304 TYR 0.012 0.001 TYR D 631 ARG 0.008 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 2.179 Fit side-chains revert: symmetry clash REVERT: A 363 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7705 (ttt-90) REVERT: A 386 CYS cc_start: 0.6832 (m) cc_final: 0.6432 (m) REVERT: A 412 MET cc_start: 0.8931 (mtm) cc_final: 0.8538 (mtm) REVERT: A 691 GLN cc_start: 0.7018 (tp40) cc_final: 0.6698 (tp40) REVERT: B 384 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8134 (mp) REVERT: C 162 MET cc_start: 0.7879 (tpp) cc_final: 0.7478 (tpp) REVERT: C 326 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8225 (mm-30) REVERT: C 572 MET cc_start: 0.7358 (ttp) cc_final: 0.6808 (tpp) REVERT: C 678 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7307 (tt) REVERT: D 306 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7996 (p) REVERT: D 310 ASN cc_start: 0.7909 (t0) cc_final: 0.7661 (t0) REVERT: D 343 SER cc_start: 0.8767 (m) cc_final: 0.8545 (m) REVERT: D 691 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6861 (mm-40) REVERT: D 716 MET cc_start: 0.4771 (pmm) cc_final: 0.3603 (mtt) outliers start: 36 outliers final: 28 residues processed: 300 average time/residue: 0.3436 time to fit residues: 154.5707 Evaluate side-chains 300 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 691 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 118 optimal weight: 0.0870 chunk 153 optimal weight: 0.0370 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20622 Z= 0.124 Angle : 0.485 7.220 27879 Z= 0.257 Chirality : 0.039 0.390 3129 Planarity : 0.004 0.048 3446 Dihedral : 10.524 158.511 2936 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.56 % Allowed : 8.88 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.95 (0.18), residues: 2449 helix: 2.19 (0.14), residues: 1363 sheet: 0.29 (0.59), residues: 76 loop : -1.66 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 740 HIS 0.003 0.001 HIS C 378 PHE 0.014 0.001 PHE A 304 TYR 0.013 0.001 TYR D 631 ARG 0.007 0.000 ARG D 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4898 Ramachandran restraints generated. 2449 Oldfield, 0 Emsley, 2449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 2.193 Fit side-chains revert: symmetry clash REVERT: A 363 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7706 (ttt-90) REVERT: A 386 CYS cc_start: 0.6863 (m) cc_final: 0.6456 (m) REVERT: A 412 MET cc_start: 0.8917 (mtm) cc_final: 0.8514 (mtm) REVERT: A 691 GLN cc_start: 0.7055 (tp40) cc_final: 0.6737 (tp40) REVERT: B 237 LYS cc_start: 0.6964 (pttt) cc_final: 0.6687 (ptpt) REVERT: B 384 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8097 (mp) REVERT: B 684 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5377 (pt0) REVERT: C 162 MET cc_start: 0.7852 (tpp) cc_final: 0.7435 (tpp) REVERT: C 326 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8237 (mm-30) REVERT: C 445 MET cc_start: 0.9236 (mmm) cc_final: 0.8737 (mmp) REVERT: C 572 MET cc_start: 0.7375 (ttp) cc_final: 0.6842 (tpp) REVERT: C 678 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7284 (tt) REVERT: D 306 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7989 (p) REVERT: D 310 ASN cc_start: 0.7890 (t0) cc_final: 0.7651 (t0) REVERT: D 343 SER cc_start: 0.8764 (m) cc_final: 0.8540 (m) REVERT: D 716 MET cc_start: 0.4751 (pmm) cc_final: 0.3510 (mtt) outliers start: 34 outliers final: 29 residues processed: 294 average time/residue: 0.3547 time to fit residues: 156.9719 Evaluate side-chains 304 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 324 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 393 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 193 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 chunk 198 optimal weight: 0.0050 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.190343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.142096 restraints weight = 21305.338| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.56 r_work: 0.3040 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 20622 Z= 0.134 Angle : 0.488 7.485 27879 Z= 0.257 Chirality : 0.039 0.388 3129 Planarity : 0.004 0.048 3446 Dihedral : 10.369 159.957 2936 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.52 % Allowed : 9.11 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 0.98 (0.18), residues: 2449 helix: 2.21 (0.14), residues: 1364 sheet: 0.33 (0.59), residues: 76 loop : -1.64 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 740 HIS 0.003 0.001 HIS C 378 PHE 0.014 0.001 PHE A 304 TYR 0.014 0.001 TYR D 631 ARG 0.007 0.000 ARG D 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.17 seconds wall clock time: 84 minutes 55.86 seconds (5095.86 seconds total)