Starting phenix.real_space_refine on Thu Dec 14 13:46:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/12_2023/7o85_12761.pdb" } resolution = 3.3 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= 0.002 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 42 5.16 5 C 17892 2.51 5 N 4991 2.21 5 O 5586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28525 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "C" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "D" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "F" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "G" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "H" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "I" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "J" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "K" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "L" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "M" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "N" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "O" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "P" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "Q" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "S" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 17, 'TRANS': 314} Chain breaks: 4 Chain: "T" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 706 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 747 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.58, per 1000 atoms: 0.48 Number of scatterers: 28525 At special positions: 0 Unit cell: (214.5, 217.8, 72.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 42 16.00 O 5586 8.00 N 4991 7.00 C 17892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 5.4 seconds 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 77 sheets defined 16.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER A 312 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER D 312 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR D 517 " --> pdb=" O PRO D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 Processing helix chain 'D' and resid 555 through 570 Processing helix chain 'D' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE D 581 " --> pdb=" O LEU D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA F 102 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER G 312 " --> pdb=" O VAL G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 487 Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR G 517 " --> pdb=" O PRO G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 531 Processing helix chain 'G' and resid 555 through 570 Processing helix chain 'G' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE G 581 " --> pdb=" O LEU G 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 614 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA I 102 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 191 Processing helix chain 'J' and resid 234 through 241 Processing helix chain 'J' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS J 253 " --> pdb=" O GLU J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER J 312 " --> pdb=" O VAL J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 487 Processing helix chain 'J' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR J 517 " --> pdb=" O PRO J 513 " (cutoff:3.500A) Processing helix chain 'J' and resid 522 through 531 Processing helix chain 'J' and resid 555 through 570 Processing helix chain 'J' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE J 581 " --> pdb=" O LEU J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 608 through 614 Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA L 102 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 191 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS M 253 " --> pdb=" O GLU M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER M 312 " --> pdb=" O VAL M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 480 through 487 Processing helix chain 'M' and resid 512 through 517 removed outlier: 3.817A pdb=" N THR M 517 " --> pdb=" O PRO M 513 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 531 Processing helix chain 'M' and resid 555 through 570 Processing helix chain 'M' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE M 581 " --> pdb=" O LEU M 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 608 through 614 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'O' and resid 98 through 102 removed outlier: 4.017A pdb=" N ALA O 102 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 191 Processing helix chain 'P' and resid 234 through 241 Processing helix chain 'P' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS P 253 " --> pdb=" O GLU P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 308 through 314 removed outlier: 4.251A pdb=" N SER P 312 " --> pdb=" O VAL P 309 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 487 Processing helix chain 'P' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR P 517 " --> pdb=" O PRO P 513 " (cutoff:3.500A) Processing helix chain 'P' and resid 522 through 531 Processing helix chain 'P' and resid 555 through 570 Processing helix chain 'P' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE P 581 " --> pdb=" O LEU P 578 " (cutoff:3.500A) Processing helix chain 'P' and resid 608 through 614 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA R 102 " --> pdb=" O ASP R 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 191 Processing helix chain 'S' and resid 234 through 241 Processing helix chain 'S' and resid 248 through 253 removed outlier: 4.060A pdb=" N HIS S 253 " --> pdb=" O GLU S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 314 removed outlier: 4.250A pdb=" N SER S 312 " --> pdb=" O VAL S 309 " (cutoff:3.500A) Processing helix chain 'S' and resid 480 through 487 Processing helix chain 'S' and resid 512 through 517 removed outlier: 3.816A pdb=" N THR S 517 " --> pdb=" O PRO S 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 522 through 531 Processing helix chain 'S' and resid 555 through 570 Processing helix chain 'S' and resid 577 through 581 removed outlier: 3.635A pdb=" N ILE S 581 " --> pdb=" O LEU S 578 " (cutoff:3.500A) Processing helix chain 'S' and resid 608 through 614 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 98 through 102 removed outlier: 4.018A pdb=" N ALA U 102 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP A 195 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 470 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 63 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 39 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 36 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 87 " --> pdb=" O TYR B 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA B 38 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ALA B 85 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA C 93 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 68 through 73 Processing sheet with id=AB3, first strand: chain 'D' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP D 195 " --> pdb=" O PHE D 202 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 296 through 297 Processing sheet with id=AB6, first strand: chain 'D' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 470 " --> pdb=" O THR D 461 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB9, first strand: chain 'D' and resid 596 through 597 removed outlier: 3.549A pdb=" N GLY D 606 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 5 removed outlier: 4.296A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA E 39 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 36 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE E 87 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA E 38 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA E 85 " --> pdb=" O ALA E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP F 47 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA F 93 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 73 Processing sheet with id=AC5, first strand: chain 'G' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP G 195 " --> pdb=" O PHE G 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 296 through 297 Processing sheet with id=AC8, first strand: chain 'G' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG G 470 " --> pdb=" O THR G 461 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'G' and resid 596 through 597 removed outlier: 3.549A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER H 63 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA H 39 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 36 " --> pdb=" O PHE H 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE H 87 " --> pdb=" O TYR H 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA H 38 " --> pdb=" O ALA H 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA H 85 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP I 47 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA I 93 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 68 through 73 Processing sheet with id=AD7, first strand: chain 'J' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP J 195 " --> pdb=" O PHE J 202 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 262 through 263 removed outlier: 3.818A pdb=" N ASN J 409 " --> pdb=" O ASN J 368 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 296 through 297 Processing sheet with id=AE1, first strand: chain 'J' and resid 458 through 462 removed outlier: 4.156A pdb=" N ILE J 459 " --> pdb=" O ASP J 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 470 " --> pdb=" O THR J 461 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE J 589 " --> pdb=" O THR J 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG J 490 " --> pdb=" O ILE J 589 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE J 591 " --> pdb=" O ARG J 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE J 492 " --> pdb=" O ILE J 591 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASP J 593 " --> pdb=" O ILE J 492 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AE4, first strand: chain 'J' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY J 606 " --> pdb=" O HIS J 597 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER K 63 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA K 39 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR K 36 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA K 38 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA K 85 " --> pdb=" O ALA K 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP L 47 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA L 93 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 68 through 73 Processing sheet with id=AE9, first strand: chain 'M' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP M 195 " --> pdb=" O PHE M 202 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN M 409 " --> pdb=" O ASN M 368 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 296 through 297 Processing sheet with id=AF3, first strand: chain 'M' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE M 459 " --> pdb=" O ASP M 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 470 " --> pdb=" O THR M 461 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE M 589 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG M 490 " --> pdb=" O ILE M 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE M 591 " --> pdb=" O ARG M 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE M 492 " --> pdb=" O ILE M 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP M 593 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 541 through 542 Processing sheet with id=AF6, first strand: chain 'M' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY M 606 " --> pdb=" O HIS M 597 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 67 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA N 39 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR N 36 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA N 38 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA N 85 " --> pdb=" O ALA N 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP O 47 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA O 93 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 68 through 73 Processing sheet with id=AG2, first strand: chain 'P' and resid 192 through 196 removed outlier: 3.519A pdb=" N ASP P 195 " --> pdb=" O PHE P 202 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN P 409 " --> pdb=" O ASN P 368 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 296 through 297 Processing sheet with id=AG5, first strand: chain 'P' and resid 458 through 462 removed outlier: 4.155A pdb=" N ILE P 459 " --> pdb=" O ASP P 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG P 470 " --> pdb=" O THR P 461 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 501 through 506 removed outlier: 8.766A pdb=" N ILE P 589 " --> pdb=" O THR P 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG P 490 " --> pdb=" O ILE P 589 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE P 591 " --> pdb=" O ARG P 490 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE P 492 " --> pdb=" O ILE P 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP P 593 " --> pdb=" O ILE P 492 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 541 through 542 Processing sheet with id=AG8, first strand: chain 'P' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY P 606 " --> pdb=" O HIS P 597 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP Q 70 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER Q 67 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER Q 63 " --> pdb=" O THR Q 74 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 39 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR Q 36 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE Q 87 " --> pdb=" O TYR Q 36 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA Q 38 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA Q 85 " --> pdb=" O ALA Q 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'R' and resid 58 through 60 removed outlier: 5.167A pdb=" N TRP R 47 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA R 93 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 68 through 73 Processing sheet with id=AH4, first strand: chain 'S' and resid 192 through 196 removed outlier: 3.520A pdb=" N ASP S 195 " --> pdb=" O PHE S 202 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'S' and resid 262 through 263 removed outlier: 3.819A pdb=" N ASN S 409 " --> pdb=" O ASN S 368 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'S' and resid 296 through 297 Processing sheet with id=AH7, first strand: chain 'S' and resid 458 through 462 removed outlier: 4.156A pdb=" N ILE S 459 " --> pdb=" O ASP S 472 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG S 470 " --> pdb=" O THR S 461 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'S' and resid 501 through 506 removed outlier: 8.765A pdb=" N ILE S 589 " --> pdb=" O THR S 488 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG S 490 " --> pdb=" O ILE S 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE S 591 " --> pdb=" O ARG S 490 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE S 492 " --> pdb=" O ILE S 591 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP S 593 " --> pdb=" O ILE S 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'S' and resid 541 through 542 Processing sheet with id=AI1, first strand: chain 'S' and resid 596 through 597 removed outlier: 3.550A pdb=" N GLY S 606 " --> pdb=" O HIS S 597 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'T' and resid 4 through 5 removed outlier: 4.297A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER T 67 " --> pdb=" O ASP T 70 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER T 63 " --> pdb=" O THR T 74 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 53 through 54 removed outlier: 5.547A pdb=" N ALA T 43 " --> pdb=" O ALA T 39 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA T 39 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR T 49 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU T 33 " --> pdb=" O TYR T 49 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR T 36 " --> pdb=" O PHE T 87 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE T 87 " --> pdb=" O TYR T 36 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA T 38 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA T 85 " --> pdb=" O ALA T 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'U' and resid 58 through 60 removed outlier: 5.168A pdb=" N TRP U 47 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA U 93 " --> pdb=" O ALA U 39 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 68 through 73 707 hydrogen bonds defined for protein. 1743 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: 10.59 Time building geometry restraints manager: 11.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9542 1.34 - 1.46: 5888 1.46 - 1.57: 13585 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 29078 Sorted by residual: bond pdb=" CA ILE K 48 " pdb=" CB ILE K 48 " ideal model delta sigma weight residual 1.540 1.551 -0.010 1.23e-02 6.61e+03 7.23e-01 bond pdb=" CA ILE T 48 " pdb=" CB ILE T 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.68e-01 bond pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.50e-01 bond pdb=" CA ILE E 48 " pdb=" CB ILE E 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.26e-01 bond pdb=" CA ILE Q 48 " pdb=" CB ILE Q 48 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.23e-02 6.61e+03 6.09e-01 ... (remaining 29073 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 789 107.33 - 114.01: 16406 114.01 - 120.69: 10833 120.69 - 127.37: 11333 127.37 - 134.05: 245 Bond angle restraints: 39606 Sorted by residual: angle pdb=" C HIS T 55 " pdb=" N SER T 56 " pdb=" CA SER T 56 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" N SER D 402 " pdb=" CA SER D 402 " pdb=" C SER D 402 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.77e+00 angle pdb=" N SER G 402 " pdb=" CA SER G 402 " pdb=" C SER G 402 " ideal model delta sigma weight residual 114.56 111.02 3.54 1.27e+00 6.20e-01 7.77e+00 angle pdb=" N SER A 402 " pdb=" CA SER A 402 " pdb=" C SER A 402 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.68e+00 angle pdb=" N SER P 402 " pdb=" CA SER P 402 " pdb=" C SER P 402 " ideal model delta sigma weight residual 114.56 111.05 3.51 1.27e+00 6.20e-01 7.65e+00 ... (remaining 39601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 15327 15.48 - 30.97: 1494 30.97 - 46.45: 336 46.45 - 61.93: 77 61.93 - 77.42: 28 Dihedral angle restraints: 17262 sinusoidal: 6020 harmonic: 11242 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.91 -48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS B 23 " pdb=" SG CYS B 23 " pdb=" SG CYS B 88 " pdb=" CB CYS B 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.91 -48.91 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " pdb=" CB CYS N 88 " ideal model delta sinusoidal sigma weight residual 93.00 141.89 -48.89 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 17259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2530 0.027 - 0.055: 1292 0.055 - 0.082: 346 0.082 - 0.110: 224 0.110 - 0.137: 109 Chirality restraints: 4501 Sorted by residual: chirality pdb=" CA ILE M 374 " pdb=" N ILE M 374 " pdb=" C ILE M 374 " pdb=" CB ILE M 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE S 374 " pdb=" N ILE S 374 " pdb=" C ILE S 374 " pdb=" CB ILE S 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE G 374 " pdb=" N ILE G 374 " pdb=" C ILE G 374 " pdb=" CB ILE G 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 4498 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 411 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 412 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR J 411 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO J 412 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 412 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 411 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO S 412 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO S 412 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 412 " 0.025 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 14 2.16 - 2.84: 9726 2.84 - 3.53: 37585 3.53 - 4.21: 63524 4.21 - 4.90: 113241 Nonbonded interactions: 224090 Sorted by model distance: nonbonded pdb=" OD2 ASP D 181 " pdb=" OE2 GLU D 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP P 181 " pdb=" OE2 GLU P 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP G 181 " pdb=" OE2 GLU G 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP M 181 " pdb=" OE2 GLU M 188 " model vdw 1.470 3.040 nonbonded pdb=" OD2 ASP S 181 " pdb=" OE2 GLU S 188 " model vdw 1.470 3.040 ... (remaining 224085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.030 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: 0.000 Extract box with map and model: 13.050 Check model and map are aligned: 0.410 Set scattering table: 0.270 Process input model: 72.880 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.440 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.002 0.030 29078 Z= 0.128 Angle : 0.480 6.416 39606 Z= 0.263 Chirality : 0.041 0.137 4501 Planarity : 0.004 0.045 5180 Dihedral : 13.511 77.416 9961 Min Nonbonded Distance : 1.470 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.25 (0.14), residues: 3745 helix: 0.49 (0.26), residues: 462 sheet: 0.17 (0.19), residues: 875 loop : -0.39 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 96 HIS 0.001 0.000 HIS M 263 PHE 0.009 0.001 PHE D 493 TYR 0.011 0.001 TYR H 50 ARG 0.003 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.4217 time to fit residues: 293.4050 Evaluate side-chains 295 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 5.9990 chunk 286 optimal weight: 0.3980 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 296 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN A 557 GLN A 601 ASN C 35 HIS D 485 GLN F 35 HIS G 454 GLN G 602 ASN I 35 HIS L 35 HIS M 541 GLN M 570 ASN O 35 HIS P 299 HIS P 408 ASN P 557 GLN R 31 ASN R 35 HIS S 541 GLN U 35 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29078 Z= 0.240 Angle : 0.515 6.104 39606 Z= 0.271 Chirality : 0.044 0.149 4501 Planarity : 0.005 0.050 5180 Dihedral : 3.888 16.935 4102 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.37 % Allowed : 7.03 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.48 (0.14), residues: 3745 helix: 0.09 (0.25), residues: 504 sheet: 0.36 (0.17), residues: 917 loop : -0.68 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 35 HIS 0.004 0.001 HIS D 263 PHE 0.010 0.001 PHE D 493 TYR 0.014 0.001 TYR A 233 ARG 0.003 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 355 time to evaluate : 3.264 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 28 residues processed: 378 average time/residue: 0.4542 time to fit residues: 261.7461 Evaluate side-chains 326 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 298 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2441 time to fit residues: 17.0152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 285 optimal weight: 0.0670 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 343 optimal weight: 0.0980 chunk 371 optimal weight: 7.9990 chunk 306 optimal weight: 0.7980 chunk 341 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN A 541 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN ** G 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS J 597 HIS M 299 HIS M 454 GLN M 570 ASN P 408 ASN ** P 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29078 Z= 0.201 Angle : 0.487 6.452 39606 Z= 0.256 Chirality : 0.043 0.151 4501 Planarity : 0.005 0.052 5180 Dihedral : 3.828 18.059 4102 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.26 % Allowed : 8.77 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.49 (0.14), residues: 3745 helix: 0.12 (0.25), residues: 504 sheet: 0.56 (0.18), residues: 889 loop : -0.78 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35 HIS 0.006 0.001 HIS J 597 PHE 0.010 0.001 PHE D 493 TYR 0.014 0.001 TYR O 52 ARG 0.003 0.000 ARG M 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 346 time to evaluate : 2.955 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 371 average time/residue: 0.4443 time to fit residues: 253.1485 Evaluate side-chains 320 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 300 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2840 time to fit residues: 14.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.8980 chunk 258 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 345 optimal weight: 1.9990 chunk 365 optimal weight: 9.9990 chunk 180 optimal weight: 0.0980 chunk 327 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS D 299 HIS ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 HIS ** G 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 597 HIS ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 597 HIS P 597 HIS S 299 HIS ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29078 Z= 0.278 Angle : 0.540 8.436 39606 Z= 0.279 Chirality : 0.045 0.157 4501 Planarity : 0.005 0.059 5180 Dihedral : 4.182 20.216 4102 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.48 % Allowed : 11.04 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.71 (0.14), residues: 3745 helix: -0.06 (0.25), residues: 497 sheet: 0.32 (0.18), residues: 889 loop : -0.89 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 35 HIS 0.007 0.001 HIS A 263 PHE 0.014 0.002 PHE D 531 TYR 0.015 0.002 TYR M 456 ARG 0.006 0.000 ARG S 592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 336 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 357 average time/residue: 0.4979 time to fit residues: 269.6181 Evaluate side-chains 339 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 312 time to evaluate : 3.127 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2526 time to fit residues: 17.3546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 272 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 252 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 602 ASN P 597 HIS P 602 ASN ** S 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29078 Z= 0.227 Angle : 0.497 7.859 39606 Z= 0.259 Chirality : 0.044 0.188 4501 Planarity : 0.005 0.057 5180 Dihedral : 4.015 20.868 4102 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.90 % Allowed : 13.49 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.76 (0.13), residues: 3745 helix: -0.02 (0.25), residues: 504 sheet: 0.47 (0.18), residues: 868 loop : -1.02 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 35 HIS 0.006 0.001 HIS A 263 PHE 0.010 0.001 PHE D 493 TYR 0.018 0.001 TYR U 52 ARG 0.004 0.000 ARG G 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7490 Ramachandran restraints generated. 3745 Oldfield, 0 Emsley, 3745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 340 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 349 average time/residue: 0.4734 time to fit residues: 251.1442 Evaluate side-chains 342 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 3.250 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4498 time to fit residues: 16.4456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 57.1238 > 50: distance: 36 - 39: 6.378 distance: 39 - 40: 15.638 distance: 39 - 45: 8.234 distance: 40 - 41: 30.281 distance: 40 - 43: 10.328 distance: 41 - 42: 30.619 distance: 41 - 46: 20.867 distance: 43 - 44: 16.236 distance: 44 - 45: 6.627 distance: 46 - 47: 5.438 distance: 47 - 48: 37.839 distance: 47 - 50: 15.274 distance: 48 - 49: 31.411 distance: 48 - 54: 8.934 distance: 50 - 51: 24.620 distance: 50 - 52: 20.051 distance: 51 - 53: 5.015 distance: 54 - 55: 34.144 distance: 55 - 56: 35.166 distance: 55 - 58: 28.670 distance: 56 - 57: 20.160 distance: 56 - 66: 21.591 distance: 58 - 59: 24.394 distance: 59 - 60: 3.382 distance: 59 - 61: 3.417 distance: 60 - 62: 9.374 distance: 61 - 63: 4.206 distance: 63 - 64: 3.780 distance: 64 - 65: 4.611 distance: 66 - 67: 37.129 distance: 67 - 68: 39.066 distance: 67 - 70: 22.201 distance: 68 - 69: 48.013 distance: 68 - 74: 26.343 distance: 70 - 71: 11.646 distance: 71 - 72: 22.386 distance: 71 - 73: 17.166 distance: 74 - 75: 32.906 distance: 75 - 76: 27.642 distance: 75 - 78: 19.477 distance: 76 - 77: 42.770 distance: 78 - 79: 29.039 distance: 78 - 80: 33.331 distance: 81 - 82: 4.422 distance: 82 - 83: 31.457 distance: 82 - 85: 44.605 distance: 83 - 84: 47.575 distance: 83 - 89: 43.112 distance: 85 - 86: 52.226 distance: 86 - 87: 12.146 distance: 86 - 88: 19.985 distance: 89 - 90: 33.028 distance: 89 - 95: 40.050 distance: 90 - 91: 21.776 distance: 90 - 93: 19.526 distance: 91 - 92: 40.229 distance: 91 - 96: 11.517 distance: 93 - 94: 22.280 distance: 94 - 95: 33.009 distance: 96 - 97: 21.256 distance: 97 - 98: 18.598 distance: 97 - 100: 7.766 distance: 98 - 99: 8.965 distance: 98 - 103: 11.822 distance: 100 - 101: 13.130 distance: 100 - 102: 5.052 distance: 103 - 104: 8.274 distance: 104 - 105: 11.568 distance: 104 - 107: 6.224 distance: 105 - 106: 6.617 distance: 107 - 108: 11.050 distance: 107 - 109: 10.087 distance: 110 - 111: 15.614 distance: 111 - 112: 19.719 distance: 111 - 114: 13.893 distance: 112 - 113: 10.963 distance: 112 - 118: 13.437 distance: 114 - 115: 14.622 distance: 115 - 116: 7.505 distance: 115 - 117: 7.057