Starting phenix.real_space_refine on Tue Dec 12 23:47:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/12_2023/8hil_34820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/12_2023/8hil_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_34820/12_2023/8hil_34820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/12_2023/8hil_34820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/12_2023/8hil_34820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hil_34820/12_2023/8hil_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.23, per 1000 atoms: 0.53 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: 8.14 Conformation dependent library (CDL) restraints added in 4.7 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: 2.86 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: 8.06 Time building geometry restraints manager: 8.89 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: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 6.830 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 63.630 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.180 ------------------------------------------------------------------------------- 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 : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 377 average time/residue: 0.4233 time to fit residues: 233.1858 Evaluate side-chains 203 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3245 time to fit residues: 7.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 74 optimal weight: 0.0670 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: 0.5920 ------------------------------------------------------------------------------- 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 A 938 HIS 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 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 652 GLN B 718 HIS B 764 ASN 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 I 110 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: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23546 Z= 0.161 Angle : 0.616 10.033 31753 Z= 0.324 Chirality : 0.044 0.172 3554 Planarity : 0.005 0.056 4099 Dihedral : 5.983 27.272 3165 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.15 % Rotamer: Outliers : 1.82 % Allowed : 7.37 % Favored : 90.81 % 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: -3.32 (0.14), residues: 2886 helix: -1.40 (0.16), residues: 843 sheet: -1.89 (0.25), residues: 399 loop : -2.83 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1058 HIS 0.007 0.001 HIS B 634 PHE 0.024 0.001 PHE A 322 TYR 0.022 0.002 TYR A 362 ARG 0.009 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 300 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 291 average time/residue: 0.3790 time to fit residues: 168.3336 Evaluate side-chains 215 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2171 time to fit residues: 12.3190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 216 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 260 optimal weight: 0.0670 chunk 281 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 258 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- 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** ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 305 ASN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 23546 Z= 0.310 Angle : 0.673 10.302 31753 Z= 0.353 Chirality : 0.046 0.202 3554 Planarity : 0.005 0.051 4099 Dihedral : 5.951 27.412 3165 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.34 % Favored : 87.53 % Rotamer: Outliers : 2.02 % Allowed : 10.20 % Favored : 87.78 % 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: -2.88 (0.15), residues: 2886 helix: -0.81 (0.17), residues: 843 sheet: -1.63 (0.26), residues: 397 loop : -2.70 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 84 HIS 0.010 0.001 HIS B 634 PHE 0.021 0.002 PHE B 586 TYR 0.030 0.002 TYR B1034 ARG 0.007 0.001 ARG B 424 *********************** 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 253 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 201 time to evaluate : 2.804 Fit side-chains outliers start: 52 outliers final: 24 residues processed: 240 average time/residue: 0.3739 time to fit residues: 141.0551 Evaluate side-chains 209 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2111 time to fit residues: 13.3453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 276 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 247 optimal weight: 0.0170 chunk 74 optimal weight: 10.0000 overall best weight: 0.9618 ------------------------------------------------------------------------------- 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** ** 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 634 HIS E 84 HIS E 91 ASN K 40 HIS K 76 HIS L 19 ASN L 28 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23546 Z= 0.165 Angle : 0.575 10.456 31753 Z= 0.301 Chirality : 0.043 0.162 3554 Planarity : 0.004 0.053 4099 Dihedral : 5.484 25.758 3165 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.43 % Favored : 89.50 % Rotamer: Outliers : 1.90 % Allowed : 10.55 % Favored : 87.55 % 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: -2.47 (0.15), residues: 2886 helix: -0.26 (0.18), residues: 841 sheet: -1.42 (0.26), residues: 388 loop : -2.55 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 84 HIS 0.008 0.001 HIS B 634 PHE 0.018 0.001 PHE A 322 TYR 0.015 0.001 TYR A 362 ARG 0.009 0.000 ARG H 144 *********************** 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 269 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 220 time to evaluate : 2.617 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 18 residues processed: 257 average time/residue: 0.3752 time to fit residues: 151.1503 Evaluate side-chains 214 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 2.664 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2123 time to fit residues: 10.9579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS ** 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** E 42 ASN L 19 ASN L 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 23546 Z= 0.533 Angle : 0.804 10.273 31753 Z= 0.420 Chirality : 0.051 0.264 3554 Planarity : 0.006 0.091 4099 Dihedral : 6.273 30.683 3165 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.03 % Favored : 85.83 % Rotamer: Outliers : 2.09 % Allowed : 12.80 % Favored : 85.10 % 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: -2.84 (0.15), residues: 2886 helix: -0.65 (0.17), residues: 822 sheet: -1.60 (0.26), residues: 376 loop : -2.73 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 84 HIS 0.010 0.002 HIS B 718 PHE 0.030 0.003 PHE B 586 TYR 0.036 0.003 TYR B1034 ARG 0.008 0.001 ARG B 625 *********************** 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 244 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 190 time to evaluate : 3.037 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 28 residues processed: 235 average time/residue: 0.3774 time to fit residues: 140.1139 Evaluate side-chains 200 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2151 time to fit residues: 15.3625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 54 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 276 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN H 129 HIS ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 23546 Z= 0.156 Angle : 0.574 8.103 31753 Z= 0.301 Chirality : 0.044 0.209 3554 Planarity : 0.004 0.083 4099 Dihedral : 5.426 26.322 3165 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.53 % Favored : 89.36 % Rotamer: Outliers : 0.70 % Allowed : 13.96 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2886 helix: -0.02 (0.19), residues: 834 sheet: -1.28 (0.27), residues: 373 loop : -2.53 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1058 HIS 0.004 0.001 HIS K 76 PHE 0.020 0.001 PHE A 322 TYR 0.023 0.001 TYR A 362 ARG 0.011 0.000 ARG H 144 *********************** 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 222 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 2.804 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 219 average time/residue: 0.3964 time to fit residues: 137.6306 Evaluate side-chains 191 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 2.772 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2218 time to fit residues: 6.2155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS A 922 GLN ** 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 714 GLN ** E 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 129 HIS L 19 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 23546 Z= 0.418 Angle : 0.728 9.331 31753 Z= 0.378 Chirality : 0.049 0.199 3554 Planarity : 0.006 0.076 4099 Dihedral : 5.938 29.534 3165 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.83 % Favored : 86.17 % Rotamer: Outliers : 1.32 % Allowed : 14.70 % Favored : 83.98 % 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: -2.57 (0.15), residues: 2886 helix: -0.34 (0.18), residues: 827 sheet: -1.38 (0.27), residues: 365 loop : -2.63 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1058 HIS 0.007 0.001 HIS B 509 PHE 0.024 0.002 PHE B 586 TYR 0.026 0.002 TYR B1034 ARG 0.007 0.001 ARG H 144 *********************** 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 220 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 2.679 Fit side-chains outliers start: 34 outliers final: 17 residues processed: 212 average time/residue: 0.3693 time to fit residues: 126.4778 Evaluate side-chains 198 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2114 time to fit residues: 10.6780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 164 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 187 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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** A1100 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 459 HIS ** B 509 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: 0.7777 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 23546 Z= 0.156 Angle : 0.582 8.979 31753 Z= 0.302 Chirality : 0.043 0.172 3554 Planarity : 0.004 0.069 4099 Dihedral : 5.292 25.969 3165 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.78 % Allowed : 15.17 % Favored : 84.06 % 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: -2.14 (0.15), residues: 2886 helix: 0.15 (0.19), residues: 840 sheet: -1.12 (0.27), residues: 373 loop : -2.45 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1058 HIS 0.004 0.001 HIS K 76 PHE 0.021 0.001 PHE H 8 TYR 0.022 0.001 TYR A 362 ARG 0.009 0.000 ARG H 144 *********************** 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 220 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 2.701 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 215 average time/residue: 0.3613 time to fit residues: 125.0580 Evaluate side-chains 197 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2174 time to fit residues: 8.1779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 0.0570 chunk 264 optimal weight: 0.9980 chunk 240 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS E 182 GLN H 129 HIS L 19 ASN L 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23546 Z= 0.168 Angle : 0.586 8.715 31753 Z= 0.301 Chirality : 0.043 0.185 3554 Planarity : 0.004 0.066 4099 Dihedral : 5.134 25.065 3165 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 0.27 % Allowed : 15.63 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2886 helix: 0.33 (0.19), residues: 832 sheet: -0.97 (0.28), residues: 371 loop : -2.36 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1058 HIS 0.004 0.001 HIS K 76 PHE 0.019 0.001 PHE A 322 TYR 0.022 0.001 TYR B 495 ARG 0.007 0.000 ARG B 424 *********************** 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 203 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 2.647 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 201 average time/residue: 0.3579 time to fit residues: 115.6979 Evaluate side-chains 184 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2061 time to fit residues: 4.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 284 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 129 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23546 Z= 0.211 Angle : 0.606 9.944 31753 Z= 0.311 Chirality : 0.044 0.194 3554 Planarity : 0.004 0.070 4099 Dihedral : 5.181 24.778 3165 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer: Outliers : 0.19 % Allowed : 15.87 % Favored : 83.94 % 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: -1.98 (0.15), residues: 2886 helix: 0.33 (0.19), residues: 833 sheet: -0.98 (0.28), residues: 360 loop : -2.37 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1058 HIS 0.004 0.001 HIS K 76 PHE 0.020 0.001 PHE H 8 TYR 0.023 0.002 TYR A 362 ARG 0.005 0.000 ARG B 625 ********************** 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 191 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 186 time to evaluate : 3.050 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 189 average time/residue: 0.3528 time to fit residues: 108.4346 Evaluate side-chains 183 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 2.754 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5508 time to fit residues: 4.6068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 69 optimal weight: 0.0870 chunk 209 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 95 optimal weight: 0.0970 chunk 233 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2160 ------------------------------------------------------------------------------- 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** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN H 129 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.105995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082818 restraints weight = 57042.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082587 restraints weight = 46768.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082996 restraints weight = 39743.958| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23546 Z= 0.188 Angle : 0.592 8.922 31753 Z= 0.304 Chirality : 0.044 0.399 3554 Planarity : 0.004 0.065 4099 Dihedral : 5.106 24.933 3165 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.08 % Allowed : 16.18 % Favored : 83.75 % 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: -1.91 (0.15), residues: 2886 helix: 0.40 (0.19), residues: 833 sheet: -0.94 (0.27), residues: 360 loop : -2.34 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1058 HIS 0.004 0.001 HIS K 76 PHE 0.018 0.001 PHE A 322 TYR 0.025 0.001 TYR A 752 ARG 0.005 0.000 ARG B 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.03 seconds wall clock time: 75 minutes 33.30 seconds (4533.30 seconds total)