Starting phenix.real_space_refine on Thu Dec 14 14:23:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o72_0638/12_2023/6o72_0638.pdb" } resolution = 3.0 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= 0.005 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 148 5.16 5 Na 8 4.78 5 C 18776 2.51 5 N 4604 2.21 5 O 5028 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ARG 655": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 775": "NH1" <-> "NH2" Residue "B ARG 841": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 880": "NH1" <-> "NH2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 653": "OE1" <-> "OE2" Residue "C ARG 655": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "C ARG 841": "NH1" <-> "NH2" Residue "C ARG 875": "NH1" <-> "NH2" Residue "C ARG 880": "NH1" <-> "NH2" Residue "C GLU 1041": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ARG 655": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 775": "NH1" <-> "NH2" Residue "D ARG 841": "NH1" <-> "NH2" Residue "D ARG 875": "NH1" <-> "NH2" Residue "D ARG 880": "NH1" <-> "NH2" Residue "D GLU 1041": "OE1" <-> "OE2" Residue "D GLU 1051": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28592 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "B" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "C" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "D" Number of atoms: 7019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 7019 Classifications: {'peptide': 858} Link IDs: {'PTRANS': 20, 'TRANS': 837} Chain breaks: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 140 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 3, 'Y01': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 129 Unusual residues: {' NA': 2, '9PE': 1, 'T14': 1, 'UND': 2, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 15.93, per 1000 atoms: 0.56 Number of scatterers: 28592 At special positions: 0 Unit cell: (128.139, 128.139, 145.083, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 148 16.00 P 4 15.00 Na 8 11.00 F 24 9.00 O 5028 8.00 N 4604 7.00 C 18776 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.88 Conformation dependent library (CDL) restraints added in 5.2 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 8 sheets defined 70.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 332 Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 358' Processing helix chain 'A' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 393 through 409 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE A 522 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN A 562 " --> pdb=" O TRP A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 675 Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS A 689 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 724 through 749 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP A 787 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 794 " --> pdb=" O ASN A 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 806 " --> pdb=" O ALA A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 827 " --> pdb=" O CYS A 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET A 849 " --> pdb=" O PRO A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 879 Processing helix chain 'A' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE A 894 " --> pdb=" O PHE A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS A 951 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN A 987 " --> pdb=" O VAL A 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'A' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1014 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1087 Processing helix chain 'A' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE A1093 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1089 through 1094' Processing helix chain 'B' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.709A pdb=" N ASN B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 313 " --> pdb=" O VAL B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 358' Processing helix chain 'B' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 393 through 409 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.676A pdb=" N ASN B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.519A pdb=" N PHE B 522 " --> pdb=" O MET B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN B 562 " --> pdb=" O TRP B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.797A pdb=" N LYS B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU B 583 " --> pdb=" O THR B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL B 652 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS B 689 " --> pdb=" O LYS B 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 691 " --> pdb=" O ILE B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 698 removed outlier: 4.357A pdb=" N GLY B 697 " --> pdb=" O PHE B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 724 through 749 Processing helix chain 'B' and resid 756 through 766 Processing helix chain 'B' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU B 773 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP B 787 " --> pdb=" O TYR B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 806 removed outlier: 3.805A pdb=" N ASP B 793 " --> pdb=" O TRP B 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 794 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 806 " --> pdb=" O ALA B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 827 " --> pdb=" O CYS B 823 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL B 828 " --> pdb=" O LEU B 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 833 " --> pdb=" O PHE B 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET B 849 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 879 Processing helix chain 'B' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE B 894 " --> pdb=" O PHE B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS B 951 " --> pdb=" O ILE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 970 removed outlier: 3.594A pdb=" N ASN B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN B 987 " --> pdb=" O VAL B 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 994 " --> pdb=" O PHE B 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1005 Processing helix chain 'B' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE B1012 " --> pdb=" O PHE B1008 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B1014 " --> pdb=" O TYR B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN B1058 " --> pdb=" O LEU B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG B1071 " --> pdb=" O GLU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1087 Processing helix chain 'B' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE B1093 " --> pdb=" O ILE B1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1089 through 1094' Processing helix chain 'C' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 167 removed outlier: 4.184A pdb=" N ILE C 160 " --> pdb=" O PHE C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.613A pdb=" N GLY C 184 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.711A pdb=" N ASN C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'C' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 361 through 374 removed outlier: 4.092A pdb=" N SER C 367 " --> pdb=" O GLU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 393 through 409 Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE C 522 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.579A pdb=" N GLN C 562 " --> pdb=" O TRP C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 570 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU C 583 " --> pdb=" O THR C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 627 removed outlier: 3.729A pdb=" N GLU C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLN C 633 " --> pdb=" O ASP C 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL C 652 " --> pdb=" O LEU C 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 654 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 662 through 675 Processing helix chain 'C' and resid 683 through 692 removed outlier: 3.889A pdb=" N CYS C 689 " --> pdb=" O LYS C 685 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 691 " --> pdb=" O ILE C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY C 697 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 722 Processing helix chain 'C' and resid 724 through 749 Processing helix chain 'C' and resid 756 through 766 Processing helix chain 'C' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP C 787 " --> pdb=" O TYR C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 794 " --> pdb=" O ASN C 790 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 799 " --> pdb=" O LEU C 795 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 827 " --> pdb=" O CYS C 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 828 " --> pdb=" O LEU C 824 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET C 849 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 879 Processing helix chain 'C' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE C 894 " --> pdb=" O PHE C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.281A pdb=" N TYR C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS C 951 " --> pdb=" O ILE C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.732A pdb=" N GLN C 987 " --> pdb=" O VAL C 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 994 " --> pdb=" O PHE C 990 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 995 " --> pdb=" O LEU C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1002 through 1005 Processing helix chain 'C' and resid 1006 through 1014 removed outlier: 4.324A pdb=" N PHE C1012 " --> pdb=" O PHE C1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C1014 " --> pdb=" O TYR C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1059 removed outlier: 3.529A pdb=" N ASN C1058 " --> pdb=" O LEU C1054 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG C1071 " --> pdb=" O GLU C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1087 Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 3.582A pdb=" N ILE C1093 " --> pdb=" O ILE C1089 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS C1094 " --> pdb=" O SER C1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1089 through 1094' Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.541A pdb=" N ASP D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 removed outlier: 4.185A pdb=" N ILE D 160 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 194 removed outlier: 3.614A pdb=" N GLY D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 300 through 313 removed outlier: 3.710A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 332 Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 353 through 358 removed outlier: 4.096A pdb=" N ILE D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 353 through 358' Processing helix chain 'D' and resid 361 through 374 removed outlier: 4.091A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 380 No H-bonds generated for 'chain 'D' and resid 378 through 380' Processing helix chain 'D' and resid 393 through 409 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.946A pdb=" N GLN D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing helix chain 'D' and resid 449 through 459 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 480 through 490 removed outlier: 3.677A pdb=" N ASN D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 505 removed outlier: 3.624A pdb=" N GLN D 501 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 524 removed outlier: 3.520A pdb=" N PHE D 522 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.580A pdb=" N GLN D 562 " --> pdb=" O TRP D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 removed outlier: 3.798A pdb=" N LYS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 570 " --> pdb=" O GLU D 566 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 593 removed outlier: 3.650A pdb=" N LEU D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 627 removed outlier: 3.730A pdb=" N GLU D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLN D 633 " --> pdb=" O ASP D 629 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 removed outlier: 3.527A pdb=" N VAL D 652 " --> pdb=" O LEU D 648 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 662 through 675 Processing helix chain 'D' and resid 683 through 692 removed outlier: 3.888A pdb=" N CYS D 689 " --> pdb=" O LYS D 685 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 691 " --> pdb=" O ILE D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 698 removed outlier: 4.358A pdb=" N GLY D 697 " --> pdb=" O PHE D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 722 Processing helix chain 'D' and resid 724 through 749 Processing helix chain 'D' and resid 756 through 766 Processing helix chain 'D' and resid 766 through 775 removed outlier: 3.689A pdb=" N GLU D 773 " --> pdb=" O LEU D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 removed outlier: 3.606A pdb=" N ASP D 787 " --> pdb=" O TYR D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 806 removed outlier: 3.804A pdb=" N ASP D 793 " --> pdb=" O TRP D 789 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR D 794 " --> pdb=" O ASN D 790 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR D 799 " --> pdb=" O LEU D 795 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 806 " --> pdb=" O ALA D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 842 removed outlier: 3.537A pdb=" N SER D 817 " --> pdb=" O SER D 813 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 827 " --> pdb=" O CYS D 823 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 833 " --> pdb=" O PHE D 829 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 842 " --> pdb=" O THR D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 850 removed outlier: 4.390A pdb=" N MET D 849 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 879 Processing helix chain 'D' and resid 889 through 894 removed outlier: 3.877A pdb=" N ILE D 894 " --> pdb=" O PHE D 890 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 901 removed outlier: 4.280A pdb=" N TYR D 898 " --> pdb=" O ILE D 894 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 957 removed outlier: 4.609A pdb=" N CYS D 951 " --> pdb=" O ILE D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 959 through 970 removed outlier: 3.595A pdb=" N ASN D 963 " --> pdb=" O ILE D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 997 removed outlier: 3.733A pdb=" N GLN D 987 " --> pdb=" O VAL D 983 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 994 " --> pdb=" O PHE D 990 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 995 " --> pdb=" O LEU D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1002 through 1005 Processing helix chain 'D' and resid 1006 through 1014 removed outlier: 4.323A pdb=" N PHE D1012 " --> pdb=" O PHE D1008 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D1014 " --> pdb=" O TYR D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1059 removed outlier: 3.530A pdb=" N ASN D1058 " --> pdb=" O LEU D1054 " (cutoff:3.500A) Processing helix chain 'D' and resid 1067 through 1072 removed outlier: 4.471A pdb=" N ARG D1071 " --> pdb=" O GLU D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1087 Processing helix chain 'D' and resid 1089 through 1094 removed outlier: 3.581A pdb=" N ILE D1093 " --> pdb=" O ILE D1089 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS D1094 " --> pdb=" O SER D1090 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1089 through 1094' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS A 107 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 253 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 109 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA A 202 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 252 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY A 204 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 170 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 205 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 172 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 135 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 295 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 137 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 292 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL A 319 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS A 294 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU A 321 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA A 296 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS B 107 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 253 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE B 109 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 202 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU B 252 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY B 204 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE B 170 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 205 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 172 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 135 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE B 295 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE B 137 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 292 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 319 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS B 294 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU B 321 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA B 296 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS C 107 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU C 253 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE C 109 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA C 202 " --> pdb=" O HIS C 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 252 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY C 204 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE C 170 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 205 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR C 172 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU C 135 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE C 295 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 137 " --> pdb=" O PHE C 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE C 292 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 319 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N CYS C 294 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU C 321 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ALA C 296 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 110 removed outlier: 6.181A pdb=" N LYS D 107 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU D 253 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE D 109 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA D 202 " --> pdb=" O HIS D 250 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU D 252 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY D 204 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 170 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE D 205 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR D 172 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU D 135 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE D 295 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE D 137 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE D 292 " --> pdb=" O CYS D 317 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL D 319 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N CYS D 294 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLU D 321 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ALA D 296 " --> pdb=" O GLU D 321 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 4320 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: 9.94 Time building geometry restraints manager: 12.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4480 1.31 - 1.44: 8218 1.44 - 1.56: 16246 1.56 - 1.69: 48 1.69 - 1.82: 244 Bond restraints: 29236 Sorted by residual: bond pdb=" CAI Y01 B1301 " pdb=" CAZ Y01 B1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 A1301 " pdb=" CAZ Y01 A1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.19e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.689 -0.357 2.00e-02 2.50e+03 3.18e+02 bond pdb=" C19 T14 C1305 " pdb=" N20 T14 C1305 " ideal model delta sigma weight residual 1.274 1.446 -0.172 2.00e-02 2.50e+03 7.35e+01 ... (remaining 29231 not shown) Histogram of bond angle deviations from ideal: 95.27 - 104.60: 340 104.60 - 113.93: 16864 113.93 - 123.26: 21043 123.26 - 132.59: 1161 132.59 - 141.92: 108 Bond angle restraints: 39516 Sorted by residual: angle pdb=" C PHE B1003 " pdb=" N PRO B1004 " pdb=" CA PRO B1004 " ideal model delta sigma weight residual 119.87 108.20 11.67 1.04e+00 9.25e-01 1.26e+02 angle pdb=" C PHE A1003 " pdb=" N PRO A1004 " pdb=" CA PRO A1004 " ideal model delta sigma weight residual 119.87 108.22 11.65 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE C1003 " pdb=" N PRO C1004 " pdb=" CA PRO C1004 " ideal model delta sigma weight residual 119.87 108.23 11.64 1.04e+00 9.25e-01 1.25e+02 angle pdb=" C PHE D1003 " pdb=" N PRO D1004 " pdb=" CA PRO D1004 " ideal model delta sigma weight residual 119.87 108.25 11.62 1.04e+00 9.25e-01 1.25e+02 angle pdb=" N HIS B 412 " pdb=" CA HIS B 412 " pdb=" C HIS B 412 " ideal model delta sigma weight residual 112.92 99.93 12.99 1.23e+00 6.61e-01 1.12e+02 ... (remaining 39511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 16775 31.24 - 62.47: 637 62.47 - 93.71: 56 93.71 - 124.95: 4 124.95 - 156.19: 4 Dihedral angle restraints: 17476 sinusoidal: 7408 harmonic: 10068 Sorted by residual: dihedral pdb=" CA SER D 638 " pdb=" C SER D 638 " pdb=" N CYS D 639 " pdb=" CA CYS D 639 " ideal model delta harmonic sigma weight residual 180.00 150.27 29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER A 638 " pdb=" C SER A 638 " pdb=" N CYS A 639 " pdb=" CA CYS A 639 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N CYS C 639 " pdb=" CA CYS C 639 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 17473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4117 0.101 - 0.202: 255 0.202 - 0.304: 19 0.304 - 0.405: 5 0.405 - 0.506: 4 Chirality restraints: 4400 Sorted by residual: chirality pdb=" CBI Y01 B1301 " pdb=" CAU Y01 B1301 " pdb=" CBE Y01 B1301 " pdb=" CBG Y01 B1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 D1301 " pdb=" CAU Y01 D1301 " pdb=" CBE Y01 D1301 " pdb=" CBG Y01 D1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CBI Y01 C1301 " pdb=" CAU Y01 C1301 " pdb=" CBE Y01 C1301 " pdb=" CBG Y01 C1301 " both_signs ideal model delta sigma weight residual False 2.94 2.43 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4397 not shown) Planarity restraints: 4816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 947 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 947 " -0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO C 948 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 948 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 948 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 947 " 0.056 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO A 948 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 948 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 948 " 0.047 5.00e-02 4.00e+02 ... (remaining 4813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 293 2.63 - 3.20: 24432 3.20 - 3.76: 44890 3.76 - 4.33: 64913 4.33 - 4.90: 101723 Nonbonded interactions: 236251 Sorted by model distance: nonbonded pdb=" O TYR D 286 " pdb=" O GLY D 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR C 286 " pdb=" O GLY C 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR A 286 " pdb=" O GLY A 288 " model vdw 2.062 3.040 nonbonded pdb=" O TYR B 286 " pdb=" O GLY B 288 " model vdw 2.063 3.040 nonbonded pdb=" OG1 THR B 115 " pdb=" OD1 ASP B 116 " model vdw 2.291 2.440 ... (remaining 236246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'B' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'C' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ selection = (chain 'D' and (resid 96 through 1094 or resid 1301 through 1303 or resid 1306)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.550 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: 8.360 Check model and map are aligned: 0.420 Set scattering table: 0.290 Process input model: 78.670 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.230 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.357 29236 Z= 0.562 Angle : 1.197 23.439 39516 Z= 0.617 Chirality : 0.059 0.506 4400 Planarity : 0.007 0.084 4816 Dihedral : 16.340 156.185 10924 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.25 (0.08), residues: 3336 helix: -4.15 (0.05), residues: 2240 sheet: -2.60 (0.35), residues: 176 loop : -3.67 (0.15), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 984 HIS 0.005 0.001 HIS C 129 PHE 0.033 0.002 PHE D 700 TYR 0.015 0.002 TYR C 286 ARG 0.013 0.001 ARG D 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 837 time to evaluate : 3.429 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 837 average time/residue: 1.2540 time to fit residues: 1246.2215 Evaluate side-chains 600 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 598 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2802 time to fit residues: 5.2212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 0.6980 chunk 257 optimal weight: 0.7980 chunk 142 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 266 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 308 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 297 GLN A 491 ASN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN A 987 GLN A1070 HIS B 297 GLN B 418 ASN B 429 GLN B 491 ASN B 851 GLN B 987 GLN C 297 GLN C 418 ASN C 429 GLN C 491 ASN C 851 GLN C 987 GLN C1070 HIS D 297 GLN D 429 GLN D 491 ASN D 851 GLN D 987 GLN D1070 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29236 Z= 0.211 Angle : 0.670 9.325 39516 Z= 0.346 Chirality : 0.042 0.196 4400 Planarity : 0.005 0.057 4816 Dihedral : 11.322 142.728 4256 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.71 % Allowed : 18.49 % Favored : 77.80 % 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: -3.42 (0.12), residues: 3336 helix: -1.76 (0.09), residues: 2260 sheet: -2.33 (0.36), residues: 176 loop : -3.13 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 673 HIS 0.006 0.001 HIS C 176 PHE 0.018 0.001 PHE C 751 TYR 0.036 0.002 TYR B 286 ARG 0.007 0.000 ARG C 998 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 694 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 62 residues processed: 749 average time/residue: 1.1503 time to fit residues: 1034.2703 Evaluate side-chains 634 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 572 time to evaluate : 3.248 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 25 residues processed: 37 average time/residue: 0.5042 time to fit residues: 31.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 210 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 309 optimal weight: 1.9990 chunk 334 optimal weight: 0.0010 chunk 275 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 380 HIS A 418 ASN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN B1070 HIS C 297 GLN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN D 297 GLN D 418 ASN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29236 Z= 0.238 Angle : 0.636 10.227 39516 Z= 0.327 Chirality : 0.042 0.181 4400 Planarity : 0.005 0.051 4816 Dihedral : 10.824 132.350 4256 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.39 % Allowed : 21.35 % Favored : 74.25 % 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 (0.13), residues: 3336 helix: -0.61 (0.10), residues: 2272 sheet: -2.19 (0.36), residues: 176 loop : -2.87 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 984 HIS 0.005 0.001 HIS B 176 PHE 0.016 0.001 PHE B 751 TYR 0.036 0.002 TYR B 286 ARG 0.008 0.000 ARG A 998 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 646 time to evaluate : 3.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 73 residues processed: 702 average time/residue: 1.1841 time to fit residues: 999.8835 Evaluate side-chains 653 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 580 time to evaluate : 3.074 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 31 residues processed: 45 average time/residue: 0.3972 time to fit residues: 32.2321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 0.9980 chunk 328 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 294 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 993 GLN B 297 GLN B 646 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN C 190 ASN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 646 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 993 GLN D 248 HIS D 297 GLN D 646 ASN D 876 GLN D 993 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.075 29236 Z= 0.204 Angle : 0.601 7.614 39516 Z= 0.311 Chirality : 0.041 0.190 4400 Planarity : 0.004 0.059 4816 Dihedral : 10.027 112.539 4256 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.37 % Allowed : 21.52 % Favored : 73.11 % 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: -1.24 (0.14), residues: 3336 helix: 0.00 (0.11), residues: 2300 sheet: -2.05 (0.36), residues: 176 loop : -2.61 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 888 HIS 0.004 0.001 HIS B 176 PHE 0.015 0.001 PHE A 514 TYR 0.033 0.002 TYR B 286 ARG 0.009 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 671 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 85 residues processed: 759 average time/residue: 1.1207 time to fit residues: 1031.7207 Evaluate side-chains 673 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 588 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 41 residues processed: 47 average time/residue: 0.4339 time to fit residues: 35.6563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.5980 chunk 186 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 280 optimal weight: 0.0170 chunk 227 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 82 optimal weight: 0.0970 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN A 993 GLN B 297 GLN B 501 GLN B 657 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 835 HIS D 993 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29236 Z= 0.172 Angle : 0.591 9.504 39516 Z= 0.303 Chirality : 0.041 0.197 4400 Planarity : 0.004 0.060 4816 Dihedral : 9.128 88.461 4256 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.01 % Allowed : 23.27 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3336 helix: 0.47 (0.11), residues: 2284 sheet: -1.88 (0.36), residues: 176 loop : -2.35 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 208 HIS 0.004 0.001 HIS B 176 PHE 0.021 0.001 PHE B 989 TYR 0.032 0.001 TYR D 763 ARG 0.011 0.000 ARG B 998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 686 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 74 residues processed: 769 average time/residue: 1.1643 time to fit residues: 1085.0563 Evaluate side-chains 679 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 605 time to evaluate : 3.521 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 39 residues processed: 37 average time/residue: 0.3597 time to fit residues: 26.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 273 optimal weight: 0.5980 chunk 152 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 172 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN A 501 GLN ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN B 297 GLN B 562 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 GLN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** C 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 297 GLN D 562 GLN ** D 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29236 Z= 0.194 Angle : 0.620 9.922 39516 Z= 0.315 Chirality : 0.041 0.195 4400 Planarity : 0.004 0.051 4816 Dihedral : 8.836 73.225 4256 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.88 % Allowed : 25.65 % Favored : 69.47 % 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: -0.33 (0.15), residues: 3336 helix: 0.71 (0.11), residues: 2284 sheet: -1.81 (0.37), residues: 176 loop : -2.25 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 208 HIS 0.003 0.001 HIS B 176 PHE 0.021 0.001 PHE D 989 TYR 0.023 0.001 TYR B 286 ARG 0.012 0.000 ARG A 998 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 650 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 150 outliers final: 78 residues processed: 750 average time/residue: 1.1522 time to fit residues: 1049.5328 Evaluate side-chains 654 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 576 time to evaluate : 3.491 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 45 residues processed: 37 average time/residue: 0.4840 time to fit residues: 32.4216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2914 > 50: distance: 17 - 22: 11.576 distance: 22 - 23: 9.039 distance: 23 - 24: 14.468 distance: 23 - 26: 5.824 distance: 24 - 25: 14.194 distance: 24 - 29: 31.225 distance: 25 - 52: 10.175 distance: 26 - 27: 25.732 distance: 26 - 28: 13.934 distance: 29 - 30: 23.726 distance: 30 - 31: 11.415 distance: 30 - 33: 17.235 distance: 31 - 32: 22.767 distance: 31 - 36: 12.735 distance: 32 - 60: 22.843 distance: 33 - 34: 11.429 distance: 33 - 35: 12.963 distance: 36 - 37: 10.609 distance: 37 - 38: 15.849 distance: 37 - 40: 19.356 distance: 38 - 39: 26.587 distance: 38 - 45: 16.355 distance: 39 - 71: 14.679 distance: 40 - 41: 11.615 distance: 41 - 42: 7.048 distance: 42 - 43: 5.624 distance: 42 - 44: 7.326 distance: 45 - 46: 14.841 distance: 46 - 47: 38.763 distance: 46 - 49: 10.725 distance: 47 - 48: 15.427 distance: 47 - 52: 11.663 distance: 48 - 80: 17.302 distance: 49 - 50: 38.032 distance: 52 - 53: 11.436 distance: 53 - 54: 8.383 distance: 53 - 56: 8.456 distance: 54 - 55: 8.092 distance: 54 - 60: 17.250 distance: 55 - 88: 5.095 distance: 56 - 57: 17.497 distance: 57 - 58: 21.601 distance: 57 - 59: 22.721 distance: 60 - 61: 12.553 distance: 61 - 62: 9.557 distance: 61 - 64: 15.176 distance: 62 - 63: 18.200 distance: 62 - 71: 16.261 distance: 63 - 100: 16.393 distance: 64 - 65: 7.779 distance: 65 - 66: 20.008 distance: 66 - 67: 4.301 distance: 67 - 68: 10.742 distance: 68 - 69: 14.667 distance: 68 - 70: 8.697 distance: 71 - 72: 11.408 distance: 72 - 73: 16.166 distance: 72 - 75: 7.483 distance: 73 - 74: 11.125 distance: 73 - 80: 15.117 distance: 75 - 76: 13.943 distance: 76 - 77: 23.289 distance: 77 - 78: 20.760 distance: 77 - 79: 22.729 distance: 80 - 81: 9.189 distance: 81 - 82: 13.394 distance: 81 - 84: 5.396 distance: 82 - 83: 12.555 distance: 82 - 88: 11.000 distance: 85 - 86: 10.760 distance: 85 - 87: 8.186 distance: 88 - 89: 8.673 distance: 89 - 90: 12.598 distance: 89 - 92: 5.994 distance: 90 - 91: 7.258 distance: 90 - 100: 14.427 distance: 92 - 93: 5.775 distance: 93 - 94: 6.021 distance: 93 - 95: 6.751 distance: 94 - 96: 3.922 distance: 95 - 97: 4.839 distance: 96 - 98: 7.622 distance: 97 - 98: 5.446 distance: 100 - 101: 9.377 distance: 101 - 102: 20.402 distance: 101 - 104: 6.261 distance: 102 - 103: 9.522 distance: 102 - 107: 14.424 distance: 104 - 105: 15.214 distance: 104 - 106: 13.619