Starting phenix.real_space_refine on Sun Feb 18 22:53:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/02_2024/8hil_34820.pdb" } resolution = 3.57 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= 0.003 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 Zn 6 6.06 5 Mg 1 5.21 5 S 142 5.16 5 C 14579 2.51 5 N 4028 2.21 5 O 4378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A ARG 920": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B PHE 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ARG 984": "NH1" <-> "NH2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 144": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I GLU 94": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23134 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6724 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 27, 'TRANS': 832} Chain breaks: 1 Chain: "B" Number of atoms: 8002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 8002 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 37, 'TRANS': 970} Chain breaks: 2 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2340 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1698 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 653 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1135 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "I" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 514 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "K" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 887 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 375 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15431 SG CYS C 91 76.731 55.598 147.524 1.00 75.40 S ATOM 15450 SG CYS C 94 77.587 53.560 144.645 1.00 96.75 S ATOM 15489 SG CYS C 100 75.271 51.423 147.930 1.00 66.88 S ATOM 20599 SG CYS I 7 44.922 48.221 22.285 1.00 87.40 S ATOM 20784 SG CYS I 29 48.546 49.829 22.974 1.00 90.52 S ATOM 20809 SG CYS I 32 48.085 46.690 19.452 1.00 97.38 S ATOM 21430 SG CYS J 10 50.155 57.966 126.372 1.00 27.07 S ATOM 21696 SG CYS J 44 48.206 59.128 123.553 1.00 29.38 S ATOM 22807 SG CYS L 12 79.164 24.060 106.723 1.00 83.08 S ATOM 22825 SG CYS L 15 78.550 20.137 106.948 1.00 81.63 S ATOM 22927 SG CYS L 29 82.023 21.779 107.275 1.00 89.69 S ATOM 22953 SG CYS L 32 80.662 20.377 104.003 1.00 30.00 S Time building chain proxies: 11.65, per 1000 atoms: 0.50 Number of scatterers: 23134 At special positions: 0 Unit cell: (121.545, 141.255, 164.25, 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) Zn 6 29.99 S 142 16.00 Mg 1 11.99 O 4378 8.00 N 4028 7.00 C 14579 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: 8.17 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2101 " pdb="ZN ZN A2101 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A2101 " - pdb=" NE2 HIS A 940 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 91 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 32 " Number of angles added : 6 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 32.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.152A pdb=" N GLU A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.503A pdb=" N CYS A 443 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.607A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.558A pdb=" N ALA A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.954A pdb=" N ASN A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 610 removed outlier: 3.827A pdb=" N ALA A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.173A pdb=" N LEU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.692A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 674 removed outlier: 3.784A pdb=" N VAL A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.675A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 684' Processing helix chain 'A' and resid 692 through 697 removed outlier: 3.819A pdb=" N VAL A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.704A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 750 through 770 Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.907A pdb=" N GLY A 776 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.512A pdb=" N THR A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.930A pdb=" N SER A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.867A pdb=" N LYS A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 904 removed outlier: 4.214A pdb=" N VAL A 899 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.543A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 969 removed outlier: 3.557A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 968 " --> pdb=" O ILE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1023 removed outlier: 3.617A pdb=" N VAL A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1028 through 1034 Processing helix chain 'A' and resid 1085 through 1093 removed outlier: 3.756A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 3.603A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1119 Processing helix chain 'A' and resid 1120 through 1141 removed outlier: 3.617A pdb=" N GLU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1140 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.096A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 removed outlier: 3.733A pdb=" N LYS A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.591A pdb=" N SER B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.671A pdb=" N PHE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.622A pdb=" N LEU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.990A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 316 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.662A pdb=" N LEU B 352 " --> pdb=" O CYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 380 removed outlier: 4.143A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 423 removed outlier: 3.667A pdb=" N GLN B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.562A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.940A pdb=" N LEU B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.968A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.587A pdb=" N LEU B 548 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 551 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 552' Processing helix chain 'B' and resid 582 through 596 removed outlier: 4.010A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN B 638 " --> pdb=" O HIS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.794A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 4.390A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.584A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.622A pdb=" N LEU B 762 " --> pdb=" O LYS B 759 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 763 " --> pdb=" O ASP B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.609A pdb=" N ASN B 928 " --> pdb=" O GLU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.720A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 953 through 967 removed outlier: 3.623A pdb=" N CYS B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.777A pdb=" N LEU C 74 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.875A pdb=" N CYS C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.544A pdb=" N ASP C 125 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.660A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.735A pdb=" N ALA C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 277 through 295 Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.688A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 39 " --> pdb=" O ARG E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.613A pdb=" N VAL E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.702A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.674A pdb=" N GLU E 119 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.664A pdb=" N LYS E 135 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 136 " --> pdb=" O THR E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 136' Processing helix chain 'E' and resid 151 through 155 removed outlier: 3.500A pdb=" N ASP E 154 " --> pdb=" O GLN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.829A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.698A pdb=" N GLN E 189 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 190' Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'F' and resid 66 through 82 removed outlier: 4.221A pdb=" N GLY F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.981A pdb=" N LYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.951A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.748A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.500A pdb=" N LEU J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.611A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.900A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 removed outlier: 4.173A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 412 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.626A pdb=" N VAL H 92 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU H 111 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE H 100 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.648A pdb=" N ILE A 561 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.610A pdb=" N GLY A 703 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 3.525A pdb=" N VAL A 790 " --> pdb=" O ARG A 798 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 798 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 876 through 880 removed outlier: 6.591A pdb=" N VAL A1071 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A1048 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP A1073 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A1046 " --> pdb=" O ASP A1073 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1075 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 916 through 918 removed outlier: 6.927A pdb=" N VAL A 917 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AB3, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.537A pdb=" N MET B 126 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY B 168 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 128 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AB5, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AB6, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.819A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB8, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AC1, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC2, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC3, first strand: chain 'B' and resid 576 through 580 removed outlier: 5.712A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 570 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 738 through 741 removed outlier: 3.840A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 766 through 772 removed outlier: 7.799A pdb=" N MET B 786 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 923 " --> pdb=" O MET B 786 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.612A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1011 through 1012 Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 19 removed outlier: 6.671A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE C 25 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.765A pdb=" N GLU C 162 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN C 59 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 164 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ARG C 170 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 51 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY C 172 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL C 49 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AD2, first strand: chain 'C' and resid 192 through 194 Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 224 Processing sheet with id=AD4, first strand: chain 'E' and resid 84 through 86 removed outlier: 3.684A pdb=" N VAL E 93 " --> pdb=" O HIS E 85 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS E 92 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU E 124 " --> pdb=" O LYS E 92 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS E 94 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU E 126 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 96 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AD7, first strand: chain 'I' and resid 15 through 17 removed outlier: 3.782A pdb=" N LEU I 26 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 88 through 89 Processing sheet with id=AD9, first strand: chain 'K' and resid 19 through 20 removed outlier: 6.717A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 11 697 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.04 Time building geometry restraints manager: 8.87 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: 5673 1.33 - 1.45: 4830 1.45 - 1.58: 12824 1.58 - 1.70: 0 1.70 - 1.82: 219 Bond restraints: 23546 Sorted by residual: bond pdb=" N VAL A 428 " pdb=" CA VAL A 428 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.27e-02 6.20e+03 9.39e+00 bond pdb=" N LEU B 248 " pdb=" CA LEU B 248 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.29e-02 6.01e+03 8.51e+00 bond pdb=" N SER B 783 " pdb=" CA SER B 783 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" N CYS A 886 " pdb=" CA CYS A 886 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.41e+00 bond pdb=" CA ASN B 180 " pdb=" C ASN B 180 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.56e-02 4.11e+03 8.39e+00 ... (remaining 23541 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.06: 387 105.06 - 112.49: 11614 112.49 - 119.92: 9248 119.92 - 127.34: 10264 127.34 - 134.77: 240 Bond angle restraints: 31753 Sorted by residual: angle pdb=" N LEU H 37 " pdb=" CA LEU H 37 " pdb=" C LEU H 37 " ideal model delta sigma weight residual 114.56 105.74 8.82 1.27e+00 6.20e-01 4.82e+01 angle pdb=" N VAL I 48 " pdb=" CA VAL I 48 " pdb=" C VAL I 48 " ideal model delta sigma weight residual 110.23 115.86 -5.63 1.04e+00 9.25e-01 2.93e+01 angle pdb=" C LYS A 889 " pdb=" N TYR A 890 " pdb=" CA TYR A 890 " ideal model delta sigma weight residual 123.93 132.16 -8.23 1.54e+00 4.22e-01 2.86e+01 angle pdb=" N GLU B 332 " pdb=" CA GLU B 332 " pdb=" C GLU B 332 " ideal model delta sigma weight residual 114.62 108.59 6.03 1.14e+00 7.69e-01 2.80e+01 angle pdb=" N SER A1061 " pdb=" CA SER A1061 " pdb=" C SER A1061 " ideal model delta sigma weight residual 113.88 107.53 6.35 1.23e+00 6.61e-01 2.66e+01 ... (remaining 31748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 13425 16.39 - 32.77: 755 32.77 - 49.16: 152 49.16 - 65.55: 17 65.55 - 81.93: 13 Dihedral angle restraints: 14362 sinusoidal: 5891 harmonic: 8471 Sorted by residual: dihedral pdb=" CA THR B 265 " pdb=" C THR B 265 " pdb=" N VAL B 266 " pdb=" CA VAL B 266 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ASP A 750 " pdb=" C ASP A 750 " pdb=" N PRO A 751 " pdb=" CA PRO A 751 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL B 233 " pdb=" C VAL B 233 " pdb=" N SER B 234 " pdb=" CA SER B 234 " ideal model delta harmonic sigma weight residual 180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 14359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3056 0.089 - 0.178: 460 0.178 - 0.268: 34 0.268 - 0.357: 2 0.357 - 0.446: 2 Chirality restraints: 3554 Sorted by residual: chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CB ILE H 5 " pdb=" CA ILE H 5 " pdb=" CG1 ILE H 5 " pdb=" CG2 ILE H 5 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB VAL A 759 " pdb=" CA VAL A 759 " pdb=" CG1 VAL A 759 " pdb=" CG2 VAL A 759 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3551 not shown) Planarity restraints: 4099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 560 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR B 560 " 0.057 2.00e-02 2.50e+03 pdb=" O THR B 560 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 561 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1034 " -0.022 2.00e-02 2.50e+03 2.32e-02 1.07e+01 pdb=" CG TYR B1034 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B1034 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B1034 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B1034 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B1034 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1034 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1034 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 27 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO E 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 28 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 4096 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 518 2.66 - 3.22: 20841 3.22 - 3.78: 33842 3.78 - 4.34: 46456 4.34 - 4.90: 75949 Nonbonded interactions: 177606 Sorted by model distance: nonbonded pdb=" O ASP A 449 " pdb="MG MG A2102 " model vdw 2.105 2.170 nonbonded pdb=" OD2 ASP A 453 " pdb="MG MG A2102 " model vdw 2.194 2.170 nonbonded pdb=" N LYS I 78 " pdb="ZN ZN I 202 " model vdw 2.200 2.310 nonbonded pdb=" O GLN B 333 " pdb=" OG1 THR B 338 " model vdw 2.245 2.440 nonbonded pdb=" OG SER B 360 " pdb=" OE1 GLN B 363 " model vdw 2.258 2.440 ... (remaining 177601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.630 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 61.370 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.007 0.134 23546 Z= 0.483 Angle : 1.118 10.217 31753 Z= 0.640 Chirality : 0.062 0.446 3554 Planarity : 0.007 0.074 4099 Dihedral : 11.196 81.934 8880 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.31 % Favored : 86.38 % Rotamer: Outliers : 1.12 % Allowed : 4.69 % Favored : 94.18 % 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: -4.62 (0.12), residues: 2886 helix: -3.15 (0.12), residues: 831 sheet: -2.53 (0.24), residues: 386 loop : -3.28 (0.13), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP F 126 HIS 0.012 0.002 HIS A 940 PHE 0.042 0.004 PHE B 391 TYR 0.055 0.003 TYR B1034 ARG 0.017 0.001 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 358 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.7300 (m-30) cc_final: 0.6829 (p0) REVERT: A 1006 MET cc_start: 0.6686 (mtm) cc_final: 0.6007 (tmm) REVERT: A 1024 LEU cc_start: 0.8598 (mm) cc_final: 0.8382 (mt) REVERT: A 1229 LEU cc_start: 0.7027 (tp) cc_final: 0.6822 (pt) REVERT: B 557 MET cc_start: 0.7058 (mmm) cc_final: 0.6605 (mpp) REVERT: B 585 TYR cc_start: 0.7981 (t80) cc_final: 0.7706 (t80) REVERT: B 1040 MET cc_start: 0.6156 (mtm) cc_final: 0.5562 (mtt) REVERT: F 98 LEU cc_start: 0.9044 (tt) cc_final: 0.8826 (mp) REVERT: H 7 MET cc_start: 0.6770 (mtt) cc_final: 0.6479 (mtt) REVERT: H 11 ILE cc_start: 0.8457 (tt) cc_final: 0.8109 (mp) REVERT: H 68 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6777 (pp) REVERT: H 97 LEU cc_start: 0.8245 (tt) cc_final: 0.8006 (tt) REVERT: I 97 MET cc_start: 0.5364 (mpt) cc_final: 0.4869 (mmt) REVERT: I 113 ARG cc_start: 0.6853 (ttt90) cc_final: 0.4961 (tpt90) outliers start: 29 outliers final: 8 residues processed: 377 average time/residue: 0.4220 time to fit residues: 231.4404 Evaluate side-chains 208 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 72 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 146 optimal weight: 0.1980 chunk 115 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS A 543 GLN A 635 HIS A 705 GLN A 747 HIS A 892 GLN A 894 ASN A 901 ASN A 923 GLN A1011 ASN ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 187 ASN B 216 GLN B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 718 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 955 GLN B 985 HIS B1011 ASN C 177 HIS C 229 GLN C 254 GLN E 91 ASN E 158 ASN H 36 ASN I 31 ASN I 41 ASN I 81 HIS K 51 HIS K 65 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23546 Z= 0.164 Angle : 0.613 9.627 31753 Z= 0.325 Chirality : 0.044 0.173 3554 Planarity : 0.005 0.056 4099 Dihedral : 6.835 58.234 3187 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.85 % Favored : 89.02 % Rotamer: Outliers : 2.06 % Allowed : 7.56 % Favored : 90.38 % 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: -3.33 (0.14), residues: 2886 helix: -1.40 (0.16), residues: 841 sheet: -1.91 (0.25), residues: 399 loop : -2.83 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1058 HIS 0.008 0.001 HIS B 634 PHE 0.023 0.001 PHE A 322 TYR 0.022 0.002 TYR A 362 ARG 0.010 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 246 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.7164 (m-30) cc_final: 0.6519 (p0) REVERT: A 645 MET cc_start: 0.5967 (ttt) cc_final: 0.5763 (tpp) REVERT: A 728 LYS cc_start: 0.7399 (ttpt) cc_final: 0.7175 (ttpt) REVERT: A 1006 MET cc_start: 0.6404 (mtm) cc_final: 0.5773 (tmm) REVERT: B 557 MET cc_start: 0.7048 (mmm) cc_final: 0.6616 (mpp) REVERT: B 585 TYR cc_start: 0.8030 (t80) cc_final: 0.7729 (t80) REVERT: B 895 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7966 (p) REVERT: C 117 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6799 (tp-100) REVERT: F 98 LEU cc_start: 0.9011 (tt) cc_final: 0.8804 (mp) REVERT: F 108 ARG cc_start: 0.7489 (ttm170) cc_final: 0.7203 (ttt180) REVERT: H 68 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6649 (pp) REVERT: I 72 LYS cc_start: 0.1899 (OUTLIER) cc_final: 0.0821 (tttt) REVERT: I 97 MET cc_start: 0.5585 (mpt) cc_final: 0.4889 (mmt) REVERT: I 113 ARG cc_start: 0.6433 (ttt90) cc_final: 0.4825 (tpt90) outliers start: 53 outliers final: 25 residues processed: 290 average time/residue: 0.3810 time to fit residues: 168.7517 Evaluate side-chains 226 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 216 optimal weight: 0.2980 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 231 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1011 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN H 35 HIS H 42 HIS K 40 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 23546 Z= 0.318 Angle : 0.676 10.167 31753 Z= 0.354 Chirality : 0.046 0.177 3554 Planarity : 0.005 0.051 4099 Dihedral : 6.487 58.402 3177 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.68 % Favored : 87.18 % Rotamer: Outliers : 2.99 % Allowed : 9.39 % Favored : 87.63 % 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: -2.94 (0.15), residues: 2886 helix: -0.83 (0.17), residues: 842 sheet: -1.67 (0.26), residues: 397 loop : -2.75 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 84 HIS 0.011 0.001 HIS B 634 PHE 0.021 0.002 PHE B 586 TYR 0.031 0.002 TYR B1034 ARG 0.010 0.001 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 202 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.7340 (m-30) cc_final: 0.6570 (p0) REVERT: A 809 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6587 (ttpp) REVERT: A 1006 MET cc_start: 0.6720 (mtm) cc_final: 0.6316 (tmm) REVERT: B 557 MET cc_start: 0.7083 (mmm) cc_final: 0.6737 (mpp) REVERT: B 585 TYR cc_start: 0.8126 (t80) cc_final: 0.7917 (t80) REVERT: B 895 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8073 (p) REVERT: C 117 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7263 (tp-100) REVERT: E 121 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6437 (pp) REVERT: F 60 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6087 (pttt) REVERT: F 98 LEU cc_start: 0.9040 (tt) cc_final: 0.8805 (mp) REVERT: H 68 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6460 (pp) REVERT: I 72 LYS cc_start: 0.1944 (OUTLIER) cc_final: 0.0541 (tttt) REVERT: I 97 MET cc_start: 0.5965 (mpt) cc_final: 0.5233 (mmt) REVERT: I 113 ARG cc_start: 0.6412 (ttt90) cc_final: 0.4641 (tpt90) REVERT: K 7 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.5042 (m-80) outliers start: 77 outliers final: 45 residues processed: 266 average time/residue: 0.3550 time to fit residues: 147.0215 Evaluate side-chains 242 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 247 optimal weight: 0.0570 chunk 74 optimal weight: 10.0000 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 91 ASN I 110 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23546 Z= 0.223 Angle : 0.601 9.849 31753 Z= 0.316 Chirality : 0.044 0.175 3554 Planarity : 0.004 0.053 4099 Dihedral : 6.163 59.697 3177 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.30 % Favored : 88.63 % Rotamer: Outliers : 3.34 % Allowed : 10.16 % Favored : 86.50 % 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: -2.56 (0.15), residues: 2886 helix: -0.34 (0.18), residues: 833 sheet: -1.50 (0.26), residues: 389 loop : -2.60 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 84 HIS 0.009 0.001 HIS B 634 PHE 0.017 0.002 PHE A 322 TYR 0.017 0.002 TYR B1034 ARG 0.007 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 213 time to evaluate : 2.670 Fit side-chains revert: symmetry clash REVERT: A 858 MET cc_start: 0.7515 (mtm) cc_final: 0.7244 (mtm) REVERT: A 1006 MET cc_start: 0.6613 (mtm) cc_final: 0.6143 (tmm) REVERT: B 557 MET cc_start: 0.6963 (mmm) cc_final: 0.6689 (mpp) REVERT: B 585 TYR cc_start: 0.8082 (t80) cc_final: 0.7865 (t80) REVERT: B 895 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8126 (p) REVERT: C 117 GLN cc_start: 0.7563 (tp-100) cc_final: 0.7263 (tp-100) REVERT: E 121 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6442 (pp) REVERT: F 60 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6089 (pttt) REVERT: F 98 LEU cc_start: 0.9029 (tt) cc_final: 0.8775 (mp) REVERT: H 68 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6621 (pp) REVERT: I 72 LYS cc_start: 0.1791 (OUTLIER) cc_final: 0.0757 (tttt) REVERT: I 97 MET cc_start: 0.6024 (mpt) cc_final: 0.5249 (mmt) REVERT: I 113 ARG cc_start: 0.6300 (ttt90) cc_final: 0.4566 (tpt90) REVERT: K 7 TYR cc_start: 0.5659 (OUTLIER) cc_final: 0.5019 (m-80) outliers start: 86 outliers final: 49 residues processed: 287 average time/residue: 0.3601 time to fit residues: 161.7904 Evaluate side-chains 249 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 137 TRP Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN E 42 ASN ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.127 23546 Z= 0.554 Angle : 0.818 9.706 31753 Z= 0.427 Chirality : 0.052 0.248 3554 Planarity : 0.006 0.080 4099 Dihedral : 6.806 58.784 3177 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.80 % Favored : 85.07 % Rotamer: Outliers : 3.88 % Allowed : 11.60 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.15), residues: 2886 helix: -0.75 (0.17), residues: 821 sheet: -1.68 (0.26), residues: 377 loop : -2.78 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 84 HIS 0.013 0.002 HIS B 634 PHE 0.029 0.003 PHE B 947 TYR 0.034 0.003 TYR B1034 ARG 0.008 0.001 ARG H 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 201 time to evaluate : 2.876 Fit side-chains REVERT: A 645 MET cc_start: 0.6432 (tpp) cc_final: 0.6057 (tpt) REVERT: B 557 MET cc_start: 0.7136 (mmm) cc_final: 0.6811 (mpp) REVERT: B 889 ASP cc_start: 0.4462 (OUTLIER) cc_final: 0.4071 (p0) REVERT: B 895 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8098 (p) REVERT: C 117 GLN cc_start: 0.7588 (tp-100) cc_final: 0.7360 (tp-100) REVERT: E 121 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6505 (pp) REVERT: F 60 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6452 (pttt) REVERT: F 98 LEU cc_start: 0.9076 (tt) cc_final: 0.8749 (mp) REVERT: F 124 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6559 (mm-30) REVERT: H 7 MET cc_start: 0.6860 (mtt) cc_final: 0.6577 (mtt) REVERT: H 11 ILE cc_start: 0.8506 (tt) cc_final: 0.8036 (mp) REVERT: H 68 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6523 (pp) REVERT: I 72 LYS cc_start: 0.2057 (OUTLIER) cc_final: 0.0810 (tttt) REVERT: I 97 MET cc_start: 0.6263 (mpt) cc_final: 0.5587 (mmt) REVERT: I 113 ARG cc_start: 0.6400 (ttt90) cc_final: 0.4574 (tpt90) REVERT: K 7 TYR cc_start: 0.5644 (OUTLIER) cc_final: 0.4711 (m-80) outliers start: 100 outliers final: 69 residues processed: 286 average time/residue: 0.3475 time to fit residues: 157.1303 Evaluate side-chains 266 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 189 time to evaluate : 2.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 13 ILE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 9 THR Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS A 938 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN H 129 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23546 Z= 0.169 Angle : 0.585 8.651 31753 Z= 0.307 Chirality : 0.044 0.195 3554 Planarity : 0.004 0.055 4099 Dihedral : 5.931 56.094 3177 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.98 % Favored : 88.95 % Rotamer: Outliers : 2.79 % Allowed : 13.34 % Favored : 83.86 % 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: -2.37 (0.15), residues: 2886 helix: -0.05 (0.19), residues: 831 sheet: -1.33 (0.27), residues: 376 loop : -2.56 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 84 HIS 0.006 0.001 HIS B 634 PHE 0.020 0.001 PHE A 322 TYR 0.023 0.001 TYR A 362 ARG 0.007 0.000 ARG H 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 208 time to evaluate : 2.900 Fit side-chains REVERT: A 645 MET cc_start: 0.6466 (tpp) cc_final: 0.6030 (tpt) REVERT: A 783 MET cc_start: 0.7650 (tpp) cc_final: 0.7430 (tpt) REVERT: A 998 LYS cc_start: 0.6405 (tptt) cc_final: 0.5731 (mptt) REVERT: A 1006 MET cc_start: 0.6783 (tmm) cc_final: 0.6404 (tmm) REVERT: B 557 MET cc_start: 0.7005 (mmm) cc_final: 0.6773 (mpp) REVERT: B 895 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 117 GLN cc_start: 0.7373 (tp-100) cc_final: 0.7115 (tp-100) REVERT: E 121 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6531 (pp) REVERT: F 60 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6173 (pttt) REVERT: F 98 LEU cc_start: 0.8910 (tt) cc_final: 0.8645 (mp) REVERT: H 7 MET cc_start: 0.6766 (mtt) cc_final: 0.6522 (mtt) REVERT: H 11 ILE cc_start: 0.8541 (tt) cc_final: 0.8064 (mp) REVERT: H 37 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6127 (mp) REVERT: H 68 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6588 (pp) REVERT: I 72 LYS cc_start: 0.2022 (OUTLIER) cc_final: 0.0857 (tttt) REVERT: I 97 MET cc_start: 0.6166 (mpt) cc_final: 0.5581 (mmt) REVERT: I 113 ARG cc_start: 0.6376 (ttt90) cc_final: 0.4518 (tpt90) REVERT: J 31 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: K 7 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.4812 (m-80) outliers start: 72 outliers final: 47 residues processed: 268 average time/residue: 0.3541 time to fit residues: 149.6438 Evaluate side-chains 246 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 202 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 129 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 23546 Z= 0.330 Angle : 0.669 9.313 31753 Z= 0.348 Chirality : 0.046 0.205 3554 Planarity : 0.005 0.053 4099 Dihedral : 6.089 54.233 3175 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.48 % Favored : 86.49 % Rotamer: Outliers : 3.10 % Allowed : 14.43 % Favored : 82.47 % 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: -2.43 (0.15), residues: 2886 helix: -0.15 (0.18), residues: 830 sheet: -1.27 (0.27), residues: 366 loop : -2.60 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1058 HIS 0.010 0.001 HIS B 634 PHE 0.020 0.002 PHE B 586 TYR 0.021 0.002 TYR A 362 ARG 0.005 0.001 ARG I 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 193 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 645 MET cc_start: 0.6399 (tpp) cc_final: 0.5986 (tpt) REVERT: A 998 LYS cc_start: 0.6659 (tptt) cc_final: 0.5906 (mptt) REVERT: A 1006 MET cc_start: 0.7032 (tmm) cc_final: 0.6649 (tmm) REVERT: B 557 MET cc_start: 0.7052 (mmm) cc_final: 0.6821 (mpp) REVERT: B 895 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 117 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7258 (tp-100) REVERT: E 121 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6503 (pp) REVERT: F 60 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6263 (pttt) REVERT: F 67 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7944 (pttp) REVERT: F 98 LEU cc_start: 0.8948 (tt) cc_final: 0.8679 (mp) REVERT: H 11 ILE cc_start: 0.8431 (tt) cc_final: 0.8051 (mp) REVERT: H 68 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6503 (pp) REVERT: I 72 LYS cc_start: 0.1920 (OUTLIER) cc_final: 0.0922 (tttt) REVERT: I 97 MET cc_start: 0.6289 (mpt) cc_final: 0.5738 (mmt) outliers start: 80 outliers final: 63 residues processed: 260 average time/residue: 0.3855 time to fit residues: 157.2518 Evaluate side-chains 255 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 186 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 164 optimal weight: 0.0170 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN H 129 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23546 Z= 0.241 Angle : 0.619 9.229 31753 Z= 0.322 Chirality : 0.045 0.205 3554 Planarity : 0.004 0.052 4099 Dihedral : 5.874 55.403 3173 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.30 % Favored : 87.66 % Rotamer: Outliers : 3.30 % Allowed : 14.47 % Favored : 82.23 % 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: -2.28 (0.15), residues: 2886 helix: 0.02 (0.18), residues: 831 sheet: -1.19 (0.27), residues: 369 loop : -2.52 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1058 HIS 0.008 0.001 HIS B 634 PHE 0.019 0.002 PHE H 8 TYR 0.021 0.002 TYR A 362 ARG 0.005 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 187 time to evaluate : 2.664 Fit side-chains revert: symmetry clash REVERT: A 645 MET cc_start: 0.6408 (tpp) cc_final: 0.6019 (tpt) REVERT: A 998 LYS cc_start: 0.6437 (tptt) cc_final: 0.5749 (mptt) REVERT: A 1006 MET cc_start: 0.6940 (tmm) cc_final: 0.6518 (tmm) REVERT: B 557 MET cc_start: 0.7037 (mmm) cc_final: 0.6816 (mpp) REVERT: B 625 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8389 (ppt170) REVERT: B 889 ASP cc_start: 0.4324 (OUTLIER) cc_final: 0.3890 (p0) REVERT: B 895 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8131 (p) REVERT: C 117 GLN cc_start: 0.7465 (tp-100) cc_final: 0.7235 (tp-100) REVERT: E 121 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6509 (pp) REVERT: F 60 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6162 (pttt) REVERT: F 67 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7965 (pttp) REVERT: F 98 LEU cc_start: 0.8929 (tt) cc_final: 0.8654 (mp) REVERT: H 37 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6142 (mp) REVERT: H 68 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6502 (pp) REVERT: I 72 LYS cc_start: 0.1902 (OUTLIER) cc_final: 0.0899 (tttt) REVERT: I 97 MET cc_start: 0.6266 (mpt) cc_final: 0.5729 (mmt) REVERT: K 7 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.4745 (m-80) outliers start: 85 outliers final: 62 residues processed: 257 average time/residue: 0.3529 time to fit residues: 144.7426 Evaluate side-chains 254 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 182 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 240 optimal weight: 0.0050 chunk 256 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 78 optimal weight: 0.0570 chunk 232 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 255 optimal weight: 0.3980 overall best weight: 2.0916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 23546 Z= 0.275 Angle : 0.636 10.115 31753 Z= 0.330 Chirality : 0.045 0.197 3554 Planarity : 0.004 0.052 4099 Dihedral : 5.867 55.635 3173 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 3.41 % Allowed : 14.47 % Favored : 82.12 % 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: -2.25 (0.15), residues: 2886 helix: 0.04 (0.18), residues: 831 sheet: -1.20 (0.27), residues: 371 loop : -2.49 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1058 HIS 0.009 0.001 HIS B 634 PHE 0.018 0.002 PHE B 947 TYR 0.020 0.002 TYR A 362 ARG 0.005 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 182 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 645 MET cc_start: 0.6394 (tpp) cc_final: 0.6070 (tpt) REVERT: A 998 LYS cc_start: 0.6437 (tptt) cc_final: 0.5749 (mptt) REVERT: A 1006 MET cc_start: 0.6935 (tmm) cc_final: 0.6489 (tmm) REVERT: B 557 MET cc_start: 0.7056 (mmm) cc_final: 0.6829 (mpp) REVERT: B 889 ASP cc_start: 0.4571 (OUTLIER) cc_final: 0.4132 (p0) REVERT: B 895 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8121 (p) REVERT: C 117 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7358 (tp-100) REVERT: E 121 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6506 (pp) REVERT: F 60 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6188 (pttt) REVERT: F 67 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8003 (pttp) REVERT: F 98 LEU cc_start: 0.8930 (tt) cc_final: 0.8630 (mp) REVERT: H 7 MET cc_start: 0.6816 (mtt) cc_final: 0.6489 (mtt) REVERT: H 37 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6040 (mp) REVERT: H 68 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6493 (pp) REVERT: I 72 LYS cc_start: 0.1909 (OUTLIER) cc_final: 0.0945 (tttt) REVERT: I 97 MET cc_start: 0.6287 (mpt) cc_final: 0.5779 (mmt) REVERT: K 7 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.4772 (m-80) outliers start: 88 outliers final: 70 residues processed: 258 average time/residue: 0.3448 time to fit residues: 141.9652 Evaluate side-chains 259 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 180 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 815 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 889 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 6.9990 chunk 271 optimal weight: 2.9990 chunk 165 optimal weight: 0.0000 chunk 128 optimal weight: 0.0570 chunk 188 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23546 Z= 0.188 Angle : 0.593 10.599 31753 Z= 0.307 Chirality : 0.044 0.196 3554 Planarity : 0.004 0.051 4099 Dihedral : 5.636 56.143 3173 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 2.91 % Allowed : 15.09 % Favored : 82.00 % 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: -2.04 (0.16), residues: 2886 helix: 0.27 (0.19), residues: 831 sheet: -1.14 (0.28), residues: 367 loop : -2.38 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1058 HIS 0.007 0.001 HIS B 634 PHE 0.018 0.001 PHE A 322 TYR 0.022 0.001 TYR H 91 ARG 0.005 0.000 ARG C 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 189 time to evaluate : 2.936 Fit side-chains REVERT: A 645 MET cc_start: 0.6422 (tpp) cc_final: 0.6145 (tpt) REVERT: A 998 LYS cc_start: 0.6190 (tptt) cc_final: 0.5815 (mptt) REVERT: A 1006 MET cc_start: 0.6818 (tmm) cc_final: 0.6336 (tmm) REVERT: B 557 MET cc_start: 0.7030 (mmm) cc_final: 0.6815 (mpp) REVERT: B 625 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8250 (ptt90) REVERT: B 895 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8121 (p) REVERT: C 117 GLN cc_start: 0.7448 (tp-100) cc_final: 0.7236 (tp-100) REVERT: E 121 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6487 (pp) REVERT: F 60 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.5992 (pttt) REVERT: F 67 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7987 (pttp) REVERT: F 98 LEU cc_start: 0.8926 (tt) cc_final: 0.8653 (mp) REVERT: H 7 MET cc_start: 0.6730 (mtt) cc_final: 0.6418 (mtt) REVERT: H 37 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6208 (mp) REVERT: H 68 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6364 (pp) REVERT: I 72 LYS cc_start: 0.1828 (OUTLIER) cc_final: 0.0903 (tttt) REVERT: I 97 MET cc_start: 0.6221 (mpt) cc_final: 0.5594 (mmt) REVERT: K 7 TYR cc_start: 0.5568 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: K 111 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8113 (tppp) outliers start: 75 outliers final: 58 residues processed: 255 average time/residue: 0.3386 time to fit residues: 138.7101 Evaluate side-chains 246 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 179 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 476 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 794 ASP Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 501 ASP Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 625 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 227 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 chunk 233 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 HIS B 492 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN L 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083673 restraints weight = 56289.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083577 restraints weight = 40823.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084196 restraints weight = 33848.238| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23546 Z= 0.137 Angle : 0.561 10.083 31753 Z= 0.288 Chirality : 0.043 0.183 3554 Planarity : 0.004 0.050 4099 Dihedral : 5.239 58.026 3173 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 2.33 % Allowed : 15.90 % Favored : 81.77 % 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: -1.83 (0.16), residues: 2886 helix: 0.50 (0.19), residues: 838 sheet: -1.01 (0.27), residues: 382 loop : -2.30 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A1058 HIS 0.006 0.001 HIS A 940 PHE 0.023 0.001 PHE A 322 TYR 0.023 0.001 TYR A 362 ARG 0.005 0.000 ARG H 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.10 seconds wall clock time: 76 minutes 48.09 seconds (4608.09 seconds total)