Starting phenix.real_space_refine on Fri Jun 28 15:03:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qqi_18592/06_2024/8qqi_18592_updated.pdb" } resolution = 2.9 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= 0.039 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 52 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 9678 2.51 5 N 2784 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 15652 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4077 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3183 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain: "C" Number of atoms: 4077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4077 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 21, 'TRANS': 495} Chain: "D" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3183 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 16, 'TRANS': 382} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 531 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 535 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'LRL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'LRL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.76, per 1000 atoms: 0.62 Number of scatterers: 15652 At special positions: 0 Unit cell: (126.48, 122.4, 128.52, 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 60 16.00 P 52 15.00 Mg 2 11.99 O 3076 8.00 N 2784 7.00 C 9678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.91 Conformation dependent library (CDL) restraints added in 2.6 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 22 sheets defined 42.7% alpha, 10.6% beta 20 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.661A pdb=" N ASP A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 24 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.754A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 90 removed outlier: 3.542A pdb=" N THR A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.660A pdb=" N ASN A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.611A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.576A pdb=" N TYR A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 388 removed outlier: 3.734A pdb=" N PHE A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 398 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.657A pdb=" N ARG A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.526A pdb=" N GLN A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 459' Processing helix chain 'A' and resid 463 through 466 removed outlier: 3.901A pdb=" N LEU A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 463 through 466' Processing helix chain 'A' and resid 470 through 493 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.576A pdb=" N ARG A 503 " --> pdb=" O MET A 499 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.705A pdb=" N SER B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 removed outlier: 3.658A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 458 through 462' Processing helix chain 'B' and resid 465 through 474 Processing helix chain 'B' and resid 502 through 517 removed outlier: 3.507A pdb=" N ILE B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 516 " --> pdb=" O THR B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 578 through 597 removed outlier: 3.850A pdb=" N LYS B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 610 removed outlier: 3.578A pdb=" N GLU B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 609 " --> pdb=" O MET B 605 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE B 610 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.851A pdb=" N SER B 621 " --> pdb=" O ALA B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 623 through 639 removed outlier: 4.242A pdb=" N GLU B 636 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 685 through 695 removed outlier: 3.637A pdb=" N ARG B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 690 " --> pdb=" O GLU B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.842A pdb=" N SER B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 731 " --> pdb=" O VAL B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 744 No H-bonds generated for 'chain 'B' and resid 742 through 744' Processing helix chain 'B' and resid 747 through 753 removed outlier: 3.507A pdb=" N TRP B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 753 " --> pdb=" O GLN B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 747 through 753' Processing helix chain 'B' and resid 770 through 781 removed outlier: 3.724A pdb=" N ASP B 774 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 775 " --> pdb=" O ILE B 771 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 799 removed outlier: 3.587A pdb=" N ASN B 795 " --> pdb=" O PHE B 791 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 797 " --> pdb=" O GLU B 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B 798 " --> pdb=" O GLU B 794 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 799 " --> pdb=" O ASN B 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 31 removed outlier: 3.660A pdb=" N ASP C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 24 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 removed outlier: 3.755A pdb=" N ARG C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 83 through 90 removed outlier: 3.543A pdb=" N THR C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.660A pdb=" N ASN C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 208 No H-bonds generated for 'chain 'C' and resid 205 through 208' Processing helix chain 'C' and resid 227 through 234 removed outlier: 3.610A pdb=" N GLU C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 313 through 321 removed outlier: 3.576A pdb=" N TYR C 321 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 388 removed outlier: 3.734A pdb=" N PHE C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 355 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE C 367 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C 368 " --> pdb=" O ARG C 364 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 398 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.656A pdb=" N ARG C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 removed outlier: 3.526A pdb=" N GLN C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 457 " --> pdb=" O GLN C 453 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 459 " --> pdb=" O ALA C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 452 through 459' Processing helix chain 'C' and resid 463 through 466 removed outlier: 3.902A pdb=" N LEU C 466 " --> pdb=" O LEU C 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 463 through 466' Processing helix chain 'C' and resid 470 through 493 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.575A pdb=" N ARG C 503 " --> pdb=" O MET C 499 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 433 removed outlier: 3.706A pdb=" N SER D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 462 removed outlier: 3.658A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 458 through 462' Processing helix chain 'D' and resid 465 through 474 Processing helix chain 'D' and resid 502 through 517 removed outlier: 3.507A pdb=" N ILE D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 516 " --> pdb=" O THR D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 578 through 597 removed outlier: 3.851A pdb=" N LYS D 582 " --> pdb=" O GLU D 578 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 610 removed outlier: 3.578A pdb=" N GLU D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 609 " --> pdb=" O MET D 605 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE D 610 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 621 removed outlier: 3.852A pdb=" N SER D 621 " --> pdb=" O ALA D 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 621' Processing helix chain 'D' and resid 623 through 639 removed outlier: 4.242A pdb=" N GLU D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 682 No H-bonds generated for 'chain 'D' and resid 679 through 682' Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.636A pdb=" N ARG D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 690 " --> pdb=" O GLU D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 731 removed outlier: 3.841A pdb=" N SER D 730 " --> pdb=" O LEU D 726 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 731 " --> pdb=" O VAL D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 744 No H-bonds generated for 'chain 'D' and resid 742 through 744' Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.508A pdb=" N TRP D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 753 " --> pdb=" O GLN D 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 747 through 753' Processing helix chain 'D' and resid 770 through 781 removed outlier: 3.725A pdb=" N ASP D 774 " --> pdb=" O ALA D 770 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN D 775 " --> pdb=" O ILE D 771 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 799 removed outlier: 3.587A pdb=" N ASN D 795 " --> pdb=" O PHE D 791 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 798 " --> pdb=" O GLU D 794 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 799 " --> pdb=" O ASN D 795 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= B, first strand: chain 'A' and resid 171 through 174 removed outlier: 3.543A pdb=" N SER A 171 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 173 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.599A pdb=" N GLU A 520 " --> pdb=" O ILE A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 237 through 243 Processing sheet with id= E, first strand: chain 'A' and resid 245 through 250 removed outlier: 3.640A pdb=" N ARG A 245 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A 263 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU A 247 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL A 261 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU A 249 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE A 259 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU A 257 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 291 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= G, first strand: chain 'A' and resid 442 through 444 removed outlier: 3.631A pdb=" N GLY A 442 " --> pdb=" O TYR A 449 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 441 through 444 removed outlier: 6.582A pdb=" N GLU B 419 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 444 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR B 421 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 542 through 546 Processing sheet with id= J, first strand: chain 'B' and resid 565 through 567 removed outlier: 3.607A pdb=" N PHE B 706 " --> pdb=" O HIS B 567 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 707 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 646 through 650 removed outlier: 3.594A pdb=" N GLN B 646 " --> pdb=" O ARG B 667 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= M, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.544A pdb=" N SER C 171 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 173 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 222 through 224 removed outlier: 6.599A pdb=" N GLU C 520 " --> pdb=" O ILE C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 237 through 243 Processing sheet with id= P, first strand: chain 'C' and resid 245 through 250 removed outlier: 3.640A pdb=" N ARG C 245 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU C 263 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU C 247 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL C 261 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLU C 249 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE C 259 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU C 257 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA C 291 " --> pdb=" O GLU C 306 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 335 through 338 Processing sheet with id= R, first strand: chain 'C' and resid 442 through 444 removed outlier: 3.632A pdb=" N GLY C 442 " --> pdb=" O TYR C 449 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 441 through 444 removed outlier: 6.582A pdb=" N GLU D 419 " --> pdb=" O ALA D 442 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU D 444 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR D 421 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 542 through 546 Processing sheet with id= U, first strand: chain 'D' and resid 565 through 567 removed outlier: 3.607A pdb=" N PHE D 706 " --> pdb=" O HIS D 567 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 707 " --> pdb=" O GLN D 714 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 646 through 650 removed outlier: 3.594A pdb=" N GLN D 646 " --> pdb=" O ARG D 667 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4053 1.33 - 1.45: 2882 1.45 - 1.57: 8877 1.57 - 1.69: 104 1.69 - 1.81: 110 Bond restraints: 16026 Sorted by residual: bond pdb=" C12 LRL A 601 " pdb=" C13 LRL A 601 " ideal model delta sigma weight residual 1.349 1.539 -0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C12 LRL C 601 " pdb=" C13 LRL C 601 " ideal model delta sigma weight residual 1.349 1.539 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C10 LRL C 601 " pdb=" N3 LRL C 601 " ideal model delta sigma weight residual 1.288 1.470 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" C10 LRL A 601 " pdb=" N3 LRL A 601 " ideal model delta sigma weight residual 1.288 1.470 -0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" C13 LRL C 601 " pdb=" N3 LRL C 601 " ideal model delta sigma weight residual 1.634 1.464 0.170 2.00e-02 2.50e+03 7.23e+01 ... (remaining 16021 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.72: 731 106.72 - 113.56: 8688 113.56 - 120.39: 6260 120.39 - 127.23: 5992 127.23 - 134.06: 219 Bond angle restraints: 21890 Sorted by residual: angle pdb=" O LRL C 601 " pdb=" S LRL C 601 " pdb=" O1 LRL C 601 " ideal model delta sigma weight residual 101.10 119.34 -18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" O LRL A 601 " pdb=" S LRL A 601 " pdb=" O1 LRL A 601 " ideal model delta sigma weight residual 101.10 119.31 -18.21 3.00e+00 1.11e-01 3.69e+01 angle pdb=" C8 LRL A 601 " pdb=" C LRL A 601 " pdb=" S LRL A 601 " ideal model delta sigma weight residual 134.48 122.00 12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C8 LRL C 601 " pdb=" C LRL C 601 " pdb=" S LRL C 601 " ideal model delta sigma weight residual 134.48 122.04 12.44 3.00e+00 1.11e-01 1.72e+01 angle pdb=" C1 LRL A 601 " pdb=" C LRL A 601 " pdb=" S LRL A 601 " ideal model delta sigma weight residual 104.49 116.85 -12.36 3.00e+00 1.11e-01 1.70e+01 ... (remaining 21885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.67: 8587 13.67 - 27.34: 687 27.34 - 41.01: 229 41.01 - 54.68: 152 54.68 - 68.36: 27 Dihedral angle restraints: 9682 sinusoidal: 4368 harmonic: 5314 Sorted by residual: dihedral pdb=" CA GLN B 657 " pdb=" C GLN B 657 " pdb=" N ASN B 658 " pdb=" CA ASN B 658 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLN D 657 " pdb=" C GLN D 657 " pdb=" N ASN D 658 " pdb=" CA ASN D 658 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ARG C 364 " pdb=" CB ARG C 364 " pdb=" CG ARG C 364 " pdb=" CD ARG C 364 " ideal model delta sinusoidal sigma weight residual -180.00 -129.22 -50.78 3 1.50e+01 4.44e-03 8.94e+00 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1618 0.036 - 0.072: 608 0.072 - 0.108: 131 0.108 - 0.144: 82 0.144 - 0.180: 11 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB ILE A 203 " pdb=" CA ILE A 203 " pdb=" CG1 ILE A 203 " pdb=" CG2 ILE A 203 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB ILE C 203 " pdb=" CA ILE C 203 " pdb=" CG1 ILE C 203 " pdb=" CG2 ILE C 203 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" C10 LRL A 601 " pdb=" C11 LRL A 601 " pdb=" C9 LRL A 601 " pdb=" N3 LRL A 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.73 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 2447 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG E 20 " -0.029 2.00e-02 2.50e+03 1.36e-02 5.55e+00 pdb=" N9 DG E 20 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG E 20 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG E 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG E 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG E 20 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG E 20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG E 20 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG E 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 42 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 43 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 42 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 43 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5197 2.88 - 3.38: 12413 3.38 - 3.89: 23350 3.89 - 4.39: 26403 4.39 - 4.90: 46637 Nonbonded interactions: 114000 Sorted by model distance: nonbonded pdb=" OG1 THR D 565 " pdb=" O GLU D 708 " model vdw 2.370 2.440 nonbonded pdb=" OG1 THR B 565 " pdb=" O GLU B 708 " model vdw 2.370 2.440 nonbonded pdb=" O LEU A 320 " pdb=" OG1 THR A 324 " model vdw 2.395 2.440 nonbonded pdb=" O LEU C 320 " pdb=" OG1 THR C 324 " model vdw 2.396 2.440 nonbonded pdb=" OE2 GLU D 424 " pdb="MG MG D 901 " model vdw 2.397 2.170 ... (remaining 113995 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 4.210 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: 0.010 Extract box with map and model: 13.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 46.660 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.005 0.190 16026 Z= 0.285 Angle : 0.656 18.239 21890 Z= 0.344 Chirality : 0.044 0.180 2450 Planarity : 0.005 0.053 2680 Dihedral : 13.258 68.355 6258 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.16), residues: 1824 helix: -2.25 (0.14), residues: 804 sheet: 0.25 (0.39), residues: 212 loop : -2.01 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 647 HIS 0.003 0.001 HIS C 45 PHE 0.012 0.001 PHE C 368 TYR 0.016 0.001 TYR D 483 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 724 ASP cc_start: 0.7765 (t70) cc_final: 0.7391 (m-30) REVERT: C 52 MET cc_start: 0.9022 (mtp) cc_final: 0.8774 (mtm) REVERT: D 461 MET cc_start: 0.8582 (ttt) cc_final: 0.8288 (ttm) outliers start: 2 outliers final: 1 residues processed: 317 average time/residue: 1.6954 time to fit residues: 576.8297 Evaluate side-chains 139 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 333 ASN A 484 GLN B 411 GLN B 465 GLN B 531 GLN B 542 GLN B 544 GLN B 652 HIS B 737 GLN C 267 GLN C 333 ASN C 484 GLN D 411 GLN D 531 GLN D 544 GLN D 554 GLN D 567 HIS D 721 GLN D 737 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16026 Z= 0.279 Angle : 0.605 9.168 21890 Z= 0.322 Chirality : 0.043 0.181 2450 Planarity : 0.005 0.054 2680 Dihedral : 14.756 85.339 2619 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.76 % Allowed : 12.63 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.96 (0.18), residues: 1824 helix: -0.74 (0.17), residues: 826 sheet: -0.60 (0.39), residues: 204 loop : -2.06 (0.18), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 725 HIS 0.006 0.002 HIS A 262 PHE 0.009 0.002 PHE A 330 TYR 0.012 0.002 TYR B 483 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 153 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: A 314 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 667 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7921 (ttp-170) REVERT: B 718 SER cc_start: 0.7748 (OUTLIER) cc_final: 0.7171 (p) REVERT: B 724 ASP cc_start: 0.7780 (t70) cc_final: 0.7373 (m-30) REVERT: B 748 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: C 23 ASP cc_start: 0.7990 (m-30) cc_final: 0.7688 (m-30) REVERT: C 285 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6949 (mtt180) REVERT: C 490 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7561 (tmm160) REVERT: D 447 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7362 (mmtt) REVERT: D 607 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8371 (mtmt) REVERT: D 640 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8156 (mtpp) outliers start: 58 outliers final: 26 residues processed: 196 average time/residue: 1.7087 time to fit residues: 361.7089 Evaluate side-chains 161 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 762 MET Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 547 LYS Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain D residue 758 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 149 optimal weight: 0.0170 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN B 569 ASN B 679 HIS C 357 HIS D 554 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16026 Z= 0.148 Angle : 0.480 8.873 21890 Z= 0.259 Chirality : 0.040 0.148 2450 Planarity : 0.004 0.046 2680 Dihedral : 14.303 86.244 2619 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.43 % Allowed : 13.73 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.19), residues: 1824 helix: 0.24 (0.18), residues: 814 sheet: -0.51 (0.40), residues: 200 loop : -1.87 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 725 HIS 0.003 0.001 HIS A 80 PHE 0.014 0.001 PHE D 706 TYR 0.010 0.001 TYR B 483 ARG 0.005 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 143 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 452 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6860 (tp30) REVERT: B 500 ASP cc_start: 0.7742 (m-30) cc_final: 0.7499 (m-30) REVERT: B 718 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7134 (p) REVERT: B 724 ASP cc_start: 0.7739 (t70) cc_final: 0.7296 (m-30) REVERT: B 748 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 23 ASP cc_start: 0.7971 (m-30) cc_final: 0.7661 (m-30) REVERT: C 285 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6893 (mtt180) REVERT: C 298 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.5632 (mptt) REVERT: D 447 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7357 (mmtt) REVERT: D 510 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8402 (mp) REVERT: D 607 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8326 (mtmt) REVERT: D 640 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8069 (mtpp) outliers start: 53 outliers final: 17 residues processed: 177 average time/residue: 1.6516 time to fit residues: 316.6139 Evaluate side-chains 149 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN B 569 ASN D 554 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16026 Z= 0.254 Angle : 0.573 11.140 21890 Z= 0.304 Chirality : 0.043 0.150 2450 Planarity : 0.005 0.053 2680 Dihedral : 14.561 86.944 2619 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.76 % Allowed : 14.83 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.19), residues: 1824 helix: 0.55 (0.19), residues: 802 sheet: -0.67 (0.39), residues: 208 loop : -1.97 (0.18), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 647 HIS 0.005 0.001 HIS A 80 PHE 0.015 0.001 PHE D 706 TYR 0.013 0.001 TYR B 483 ARG 0.005 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 121 time to evaluate : 1.444 Fit side-chains REVERT: A 121 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7692 (mtp180) REVERT: A 201 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: B 667 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7919 (ttp-170) REVERT: B 718 SER cc_start: 0.7818 (OUTLIER) cc_final: 0.7288 (p) REVERT: B 724 ASP cc_start: 0.7737 (t70) cc_final: 0.7366 (m-30) REVERT: B 748 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: C 285 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6947 (mtt180) REVERT: C 298 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.5665 (mptt) REVERT: C 490 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7392 (ttm170) REVERT: C 511 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 447 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7434 (mmtt) REVERT: D 552 MET cc_start: 0.8634 (tpt) cc_final: 0.8341 (tpt) REVERT: D 607 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8412 (mtmt) REVERT: D 640 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8293 (mtpp) outliers start: 58 outliers final: 30 residues processed: 163 average time/residue: 1.6787 time to fit residues: 295.8846 Evaluate side-chains 155 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 115 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 151 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN B 569 ASN D 554 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16026 Z= 0.143 Angle : 0.471 9.363 21890 Z= 0.253 Chirality : 0.039 0.146 2450 Planarity : 0.004 0.046 2680 Dihedral : 14.257 86.502 2619 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.78 % Allowed : 15.87 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.19), residues: 1824 helix: 0.95 (0.19), residues: 800 sheet: -0.34 (0.40), residues: 192 loop : -1.88 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 647 HIS 0.002 0.001 HIS A 80 PHE 0.015 0.001 PHE D 706 TYR 0.013 0.001 TYR B 483 ARG 0.005 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 1.582 Fit side-chains REVERT: A 121 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7686 (mtp180) REVERT: A 256 ARG cc_start: 0.6835 (mmm160) cc_final: 0.6555 (mmt180) REVERT: B 718 SER cc_start: 0.7821 (OUTLIER) cc_final: 0.7303 (p) REVERT: B 724 ASP cc_start: 0.7695 (t70) cc_final: 0.7248 (m-30) REVERT: B 748 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: C 23 ASP cc_start: 0.7938 (m-30) cc_final: 0.7670 (m-30) REVERT: C 285 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6944 (mtt180) REVERT: C 298 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.5523 (mptt) REVERT: D 447 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7433 (mmtt) REVERT: D 607 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8386 (mtmt) REVERT: D 640 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8227 (mtpp) outliers start: 43 outliers final: 23 residues processed: 153 average time/residue: 1.5883 time to fit residues: 264.7635 Evaluate side-chains 147 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN C 12 ASN D 554 GLN D 714 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16026 Z= 0.215 Angle : 0.532 8.347 21890 Z= 0.284 Chirality : 0.041 0.149 2450 Planarity : 0.004 0.050 2680 Dihedral : 14.446 86.751 2619 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.63 % Allowed : 15.22 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.19), residues: 1824 helix: 0.97 (0.19), residues: 802 sheet: -0.51 (0.39), residues: 196 loop : -1.95 (0.18), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.004 0.001 HIS A 80 PHE 0.015 0.001 PHE D 706 TYR 0.014 0.001 TYR B 483 ARG 0.003 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 117 time to evaluate : 1.994 Fit side-chains REVERT: A 121 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: A 201 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: B 635 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 667 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7817 (ttp-170) REVERT: B 718 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7428 (p) REVERT: B 724 ASP cc_start: 0.7712 (t70) cc_final: 0.7265 (m-30) REVERT: B 748 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: C 23 ASP cc_start: 0.7913 (m-30) cc_final: 0.7594 (m-30) REVERT: C 285 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6963 (mtt180) REVERT: C 298 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.5493 (mptt) REVERT: C 490 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7364 (tmm160) REVERT: C 511 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: D 447 LYS cc_start: 0.7866 (mtmm) cc_final: 0.7429 (mmtt) REVERT: D 580 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6318 (tp) REVERT: D 607 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8442 (mtmt) REVERT: D 640 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (mtpp) outliers start: 56 outliers final: 29 residues processed: 158 average time/residue: 1.6311 time to fit residues: 278.9275 Evaluate side-chains 154 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 416 GLN Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16026 Z= 0.175 Angle : 0.499 8.972 21890 Z= 0.267 Chirality : 0.040 0.147 2450 Planarity : 0.004 0.048 2680 Dihedral : 14.336 86.629 2619 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.24 % Allowed : 15.93 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.19), residues: 1824 helix: 1.16 (0.19), residues: 794 sheet: -0.51 (0.39), residues: 196 loop : -1.93 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 262 PHE 0.011 0.001 PHE A 368 TYR 0.013 0.001 TYR B 483 ARG 0.005 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 118 time to evaluate : 1.737 Fit side-chains REVERT: A 121 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7731 (mtp180) REVERT: B 635 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8870 (p) REVERT: B 667 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8254 (ttm170) REVERT: B 718 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7397 (p) REVERT: B 724 ASP cc_start: 0.7704 (t70) cc_final: 0.7250 (m-30) REVERT: B 748 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: C 23 ASP cc_start: 0.7916 (m-30) cc_final: 0.7597 (m-30) REVERT: C 121 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6762 (mtm-85) REVERT: C 285 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6970 (mtt180) REVERT: C 298 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5462 (mptt) REVERT: C 490 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7288 (tmm160) REVERT: C 511 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: D 447 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7477 (mmtt) REVERT: D 580 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6418 (tp) REVERT: D 607 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8410 (mtmt) outliers start: 50 outliers final: 26 residues processed: 155 average time/residue: 1.6670 time to fit residues: 279.3490 Evaluate side-chains 151 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16026 Z= 0.171 Angle : 0.493 8.892 21890 Z= 0.265 Chirality : 0.040 0.145 2450 Planarity : 0.004 0.048 2680 Dihedral : 14.316 86.612 2619 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.17 % Allowed : 16.39 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.19), residues: 1824 helix: 1.22 (0.19), residues: 796 sheet: -0.48 (0.40), residues: 192 loop : -1.92 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 PHE 0.014 0.001 PHE D 706 TYR 0.013 0.001 TYR B 483 ARG 0.003 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.767 Fit side-chains REVERT: A 121 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7733 (mtp180) REVERT: A 201 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 309 ARG cc_start: 0.6804 (mmm-85) cc_final: 0.6546 (mmm-85) REVERT: A 452 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6598 (tp30) REVERT: B 635 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 667 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8252 (ttm170) REVERT: B 718 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 724 ASP cc_start: 0.7712 (t70) cc_final: 0.7246 (m-30) REVERT: B 748 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 23 ASP cc_start: 0.7904 (m-30) cc_final: 0.7588 (m-30) REVERT: C 121 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6873 (mtm-85) REVERT: C 285 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6920 (mtt180) REVERT: C 298 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.5410 (mptt) REVERT: C 490 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7269 (tmm160) REVERT: C 511 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: D 447 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7527 (mmtt) outliers start: 49 outliers final: 30 residues processed: 149 average time/residue: 1.6403 time to fit residues: 266.4430 Evaluate side-chains 157 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 511 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 593 MET Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 724 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 165 optimal weight: 0.0070 chunk 99 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16026 Z= 0.127 Angle : 0.454 8.646 21890 Z= 0.244 Chirality : 0.039 0.152 2450 Planarity : 0.004 0.044 2680 Dihedral : 14.166 86.110 2619 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.40 % Allowed : 17.29 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.20), residues: 1824 helix: 1.41 (0.19), residues: 796 sheet: -0.50 (0.40), residues: 188 loop : -1.81 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 399 PHE 0.011 0.001 PHE A 368 TYR 0.011 0.001 TYR B 483 ARG 0.009 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.815 Fit side-chains REVERT: A 121 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7722 (mtp180) REVERT: A 390 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6407 (mt) REVERT: A 452 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6586 (tp30) REVERT: B 500 ASP cc_start: 0.7641 (m-30) cc_final: 0.7394 (m-30) REVERT: B 554 GLN cc_start: 0.7570 (tt0) cc_final: 0.6893 (tm-30) REVERT: B 635 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 667 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8140 (ttm170) REVERT: B 718 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7396 (p) REVERT: B 724 ASP cc_start: 0.7705 (t70) cc_final: 0.7232 (m-30) REVERT: B 748 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: C 23 ASP cc_start: 0.7898 (m-30) cc_final: 0.7627 (m-30) REVERT: C 121 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6887 (mtm-85) REVERT: C 285 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6953 (mtt180) REVERT: C 298 LYS cc_start: 0.6473 (OUTLIER) cc_final: 0.5367 (mptt) REVERT: D 447 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7521 (mmtt) REVERT: D 510 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8463 (mp) outliers start: 37 outliers final: 22 residues processed: 143 average time/residue: 1.6430 time to fit residues: 254.5248 Evaluate side-chains 149 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 650 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16026 Z= 0.162 Angle : 0.485 8.943 21890 Z= 0.260 Chirality : 0.040 0.154 2450 Planarity : 0.004 0.046 2680 Dihedral : 14.260 86.594 2619 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 17.23 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.19), residues: 1824 helix: 1.39 (0.19), residues: 798 sheet: -0.42 (0.40), residues: 192 loop : -1.87 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 80 PHE 0.016 0.001 PHE D 706 TYR 0.012 0.001 TYR B 483 ARG 0.006 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.814 Fit side-chains REVERT: A 121 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (mtp180) REVERT: A 201 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: A 452 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: B 554 GLN cc_start: 0.7576 (tt0) cc_final: 0.6896 (tm-30) REVERT: B 635 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8845 (p) REVERT: B 667 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8166 (ttm170) REVERT: B 718 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7453 (p) REVERT: B 724 ASP cc_start: 0.7718 (t70) cc_final: 0.7243 (m-30) REVERT: B 748 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: C 23 ASP cc_start: 0.7938 (m-30) cc_final: 0.7604 (m-30) REVERT: C 121 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6887 (mtm-85) REVERT: C 285 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6959 (mtt180) REVERT: C 298 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5459 (mptt) REVERT: D 447 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7540 (mmtt) outliers start: 38 outliers final: 25 residues processed: 150 average time/residue: 1.6454 time to fit residues: 267.5782 Evaluate side-chains 153 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 718 SER Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 476 CYS Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 558 SER Chi-restraints excluded: chain D residue 640 LYS Chi-restraints excluded: chain D residue 650 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 146 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 ASN D 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115285 restraints weight = 19572.697| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.80 r_work: 0.3176 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16026 Z= 0.127 Angle : 0.459 9.365 21890 Z= 0.247 Chirality : 0.039 0.152 2450 Planarity : 0.004 0.042 2680 Dihedral : 14.189 86.236 2619 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.94 % Allowed : 18.01 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.20), residues: 1824 helix: 1.56 (0.19), residues: 796 sheet: -0.47 (0.40), residues: 188 loop : -1.78 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 647 HIS 0.003 0.001 HIS A 399 PHE 0.011 0.001 PHE A 368 TYR 0.012 0.001 TYR B 483 ARG 0.007 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5672.18 seconds wall clock time: 99 minutes 29.34 seconds (5969.34 seconds total)