Starting phenix.real_space_refine on Sat Apr 13 10:35:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/04_2024/7o85_12761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/04_2024/7o85_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_12761/04_2024/7o85_12761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/04_2024/7o85_12761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/04_2024/7o85_12761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o85_12761/04_2024/7o85_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.61, per 1000 atoms: 0.51 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: 10.30 Conformation dependent library (CDL) restraints added in 5.1 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: 3.29 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: 10.28 Time building geometry restraints manager: 11.25 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: 3.390 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: 0.030 Extract box with map and model: 14.130 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 72.000 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.340 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.680 ------------------------------------------------------------------------------- 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 : 2.907 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 REVERT: A 449 ARG cc_start: 0.6882 (mtm180) cc_final: 0.6405 (pmt-80) REVERT: D 590 LEU cc_start: 0.7806 (tp) cc_final: 0.7516 (tp) REVERT: E 35 TRP cc_start: 0.6151 (m100) cc_final: 0.5912 (m100) REVERT: H 35 TRP cc_start: 0.6295 (m100) cc_final: 0.6052 (m100) REVERT: P 602 ASN cc_start: 0.6488 (t0) cc_final: 0.6070 (t0) REVERT: R 31 ASN cc_start: 0.7763 (t0) cc_final: 0.7556 (t0) REVERT: S 449 ARG cc_start: 0.6849 (mtm180) cc_final: 0.6296 (pmt-80) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.4255 time to fit residues: 294.2585 Evaluate side-chains 297 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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 35 HIS S 541 GLN U 35 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29078 Z= 0.236 Angle : 0.510 5.947 39606 Z= 0.268 Chirality : 0.044 0.148 4501 Planarity : 0.005 0.051 5180 Dihedral : 3.830 16.922 4102 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.30 % Allowed : 6.93 % Favored : 91.77 % 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: -0.45 (0.14), residues: 3745 helix: 0.14 (0.25), residues: 504 sheet: 0.39 (0.17), residues: 917 loop : -0.67 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 35 HIS 0.004 0.001 HIS S 263 PHE 0.010 0.001 PHE A 531 TYR 0.014 0.001 TYR A 233 ARG 0.003 0.000 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 391 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 355 time to evaluate : 2.946 Fit side-chains revert: symmetry clash REVERT: A 449 ARG cc_start: 0.6926 (mtm180) cc_final: 0.6241 (pmt-80) REVERT: A 601 ASN cc_start: 0.7186 (OUTLIER) cc_final: 0.6515 (t0) REVERT: D 541 GLN cc_start: 0.8611 (mt0) cc_final: 0.8396 (mt0) REVERT: G 541 GLN cc_start: 0.8458 (mt0) cc_final: 0.7590 (mt0) REVERT: G 601 ASN cc_start: 0.7124 (OUTLIER) cc_final: 0.6865 (t0) REVERT: J 214 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8198 (mtpt) REVERT: P 250 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6685 (mt-10) REVERT: P 449 ARG cc_start: 0.6933 (mtm180) cc_final: 0.6294 (pmt-80) REVERT: R 98 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7758 (ttp-170) REVERT: S 449 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6291 (pmt-80) outliers start: 36 outliers final: 29 residues processed: 376 average time/residue: 0.4857 time to fit residues: 276.9997 Evaluate side-chains 339 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 308 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 601 ASN Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 570 ASN Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 590 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 285 optimal weight: 0.1980 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 343 optimal weight: 0.5980 chunk 371 optimal weight: 7.9990 chunk 306 optimal weight: 0.7980 chunk 341 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 ASN D 454 GLN ** G 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 299 HIS J 597 HIS M 299 HIS M 454 GLN P 408 ASN ** P 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 557 GLN R 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29078 Z= 0.222 Angle : 0.498 6.818 39606 Z= 0.261 Chirality : 0.043 0.147 4501 Planarity : 0.005 0.052 5180 Dihedral : 3.880 18.045 4102 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.24 % Allowed : 8.41 % Favored : 89.36 % 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: -0.52 (0.14), residues: 3745 helix: 0.06 (0.25), residues: 504 sheet: 0.56 (0.18), residues: 882 loop : -0.80 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 35 HIS 0.007 0.001 HIS P 263 PHE 0.010 0.001 PHE D 493 TYR 0.015 0.001 TYR O 52 ARG 0.004 0.000 ARG A 600 *********************** 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 400 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 338 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: A 449 ARG cc_start: 0.6963 (mtm180) cc_final: 0.6255 (pmt-80) REVERT: B 52 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7290 (t) REVERT: G 297 ARG cc_start: 0.7156 (tpt-90) cc_final: 0.6743 (mtp180) REVERT: G 570 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.7094 (t0) REVERT: J 214 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8017 (mtpt) REVERT: P 449 ARG cc_start: 0.6931 (mtm180) cc_final: 0.6318 (pmt-80) REVERT: Q 52 SER cc_start: 0.7920 (t) cc_final: 0.7712 (t) REVERT: S 449 ARG cc_start: 0.6916 (mtm180) cc_final: 0.6349 (pmt-80) REVERT: S 590 LEU cc_start: 0.8472 (tp) cc_final: 0.8170 (tp) outliers start: 62 outliers final: 43 residues processed: 379 average time/residue: 0.4691 time to fit residues: 274.6020 Evaluate side-chains 350 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 305 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 570 ASN Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 590 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.0870 chunk 258 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 345 optimal weight: 0.7980 chunk 365 optimal weight: 7.9990 chunk 180 optimal weight: 0.0060 chunk 327 optimal weight: 0.8980 chunk 98 optimal weight: 50.0000 overall best weight: 0.5374 ------------------------------------------------------------------------------- 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** D 299 HIS G 299 HIS ** G 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 ASN M 597 HIS P 408 ASN P 597 HIS S 299 HIS S 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29078 Z= 0.189 Angle : 0.479 6.817 39606 Z= 0.251 Chirality : 0.043 0.142 4501 Planarity : 0.004 0.054 5180 Dihedral : 3.816 18.453 4102 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.13 % Allowed : 9.63 % Favored : 88.24 % 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: -0.56 (0.14), residues: 3745 helix: 0.12 (0.25), residues: 504 sheet: 0.51 (0.18), residues: 882 loop : -0.84 (0.13), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 35 HIS 0.006 0.001 HIS M 597 PHE 0.009 0.001 PHE D 493 TYR 0.019 0.001 TYR U 52 ARG 0.005 0.000 ARG D 449 *********************** 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 390 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 331 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7025 (mtm180) cc_final: 0.6307 (pmt-80) REVERT: B 52 SER cc_start: 0.7730 (t) cc_final: 0.7358 (t) REVERT: D 204 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7873 (m) REVERT: J 214 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7965 (mtpt) REVERT: P 449 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6299 (pmt-80) REVERT: Q 52 SER cc_start: 0.7949 (t) cc_final: 0.7736 (t) REVERT: S 204 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8100 (m) REVERT: S 449 ARG cc_start: 0.6982 (mtm180) cc_final: 0.6386 (pmt-80) outliers start: 59 outliers final: 48 residues processed: 365 average time/residue: 0.4565 time to fit residues: 255.8951 Evaluate side-chains 359 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 309 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 570 ASN Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.0010 chunk 207 optimal weight: 0.2980 chunk 5 optimal weight: 0.0000 chunk 272 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 311 optimal weight: 9.9990 chunk 252 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 597 HIS ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 454 GLN ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 597 HIS S 597 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29078 Z= 0.162 Angle : 0.464 6.486 39606 Z= 0.243 Chirality : 0.043 0.138 4501 Planarity : 0.004 0.055 5180 Dihedral : 3.701 18.552 4102 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.24 % Allowed : 11.26 % Favored : 86.51 % 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: -0.50 (0.14), residues: 3745 helix: 0.21 (0.25), residues: 504 sheet: 0.61 (0.18), residues: 875 loop : -0.84 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.007 0.001 HIS G 597 PHE 0.009 0.001 PHE D 493 TYR 0.015 0.001 TYR F 32 ARG 0.004 0.000 ARG A 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 390 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 328 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6253 (pmt-80) REVERT: B 52 SER cc_start: 0.7781 (t) cc_final: 0.7385 (t) REVERT: C 70 LEU cc_start: 0.8402 (mt) cc_final: 0.7895 (mt) REVERT: J 214 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8032 (mtpt) REVERT: P 449 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6303 (pmt-80) REVERT: S 297 ARG cc_start: 0.6645 (mtp180) cc_final: 0.6394 (tpt-90) REVERT: S 449 ARG cc_start: 0.6992 (mtm180) cc_final: 0.6393 (pmt-80) REVERT: S 590 LEU cc_start: 0.8458 (tp) cc_final: 0.8221 (tp) outliers start: 62 outliers final: 54 residues processed: 363 average time/residue: 0.4387 time to fit residues: 246.9448 Evaluate side-chains 367 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 313 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 52 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 587 MET Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain T residue 69 THR Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 4.9990 chunk 329 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 214 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 365 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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** A 597 HIS D 485 GLN D 553 ASN D 597 HIS G 553 ASN J 454 GLN ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29078 Z= 0.195 Angle : 0.479 7.121 39606 Z= 0.249 Chirality : 0.043 0.232 4501 Planarity : 0.004 0.058 5180 Dihedral : 3.775 19.305 4102 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.31 % Allowed : 12.19 % Favored : 85.50 % 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: -0.57 (0.14), residues: 3745 helix: 0.16 (0.25), residues: 504 sheet: 0.55 (0.18), residues: 875 loop : -0.87 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.006 0.001 HIS D 597 PHE 0.009 0.001 PHE D 493 TYR 0.014 0.001 TYR F 32 ARG 0.003 0.000 ARG D 449 *********************** REFINEMENT MACRO_CYCLE 6 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 389 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 325 time to evaluate : 3.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6305 (pmt-80) REVERT: B 52 SER cc_start: 0.7688 (t) cc_final: 0.7285 (t) REVERT: C 70 LEU cc_start: 0.8467 (mt) cc_final: 0.7973 (mt) REVERT: D 204 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7862 (m) REVERT: G 472 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: J 214 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7965 (mtpt) REVERT: M 602 ASN cc_start: 0.7041 (t0) cc_final: 0.6776 (t0) REVERT: P 185 ASP cc_start: 0.7590 (m-30) cc_final: 0.7349 (m-30) REVERT: P 449 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6321 (pmt-80) REVERT: P 579 ASP cc_start: 0.7709 (t0) cc_final: 0.7503 (t0) REVERT: P 602 ASN cc_start: 0.6410 (t0) cc_final: 0.6116 (t0) REVERT: S 449 ARG cc_start: 0.6942 (mtm180) cc_final: 0.6356 (pmt-80) REVERT: S 541 GLN cc_start: 0.8565 (mt0) cc_final: 0.8300 (mt0) outliers start: 64 outliers final: 57 residues processed: 364 average time/residue: 0.4674 time to fit residues: 261.0786 Evaluate side-chains 372 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 313 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 206 optimal weight: 50.0000 chunk 307 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 364 optimal weight: 0.3980 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A 601 ASN ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 HIS M 541 GLN ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2930 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= 0.214 Angle : 0.493 7.602 39606 Z= 0.256 Chirality : 0.044 0.214 4501 Planarity : 0.004 0.059 5180 Dihedral : 3.871 20.448 4102 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 12.81 % Favored : 84.31 % 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: -0.65 (0.13), residues: 3745 helix: 0.10 (0.25), residues: 504 sheet: 0.58 (0.17), residues: 882 loop : -0.98 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.006 0.001 HIS J 597 PHE 0.010 0.001 PHE D 531 TYR 0.015 0.001 TYR F 32 ARG 0.004 0.000 ARG G 297 *********************** REFINEMENT MACRO_CYCLE 7 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 414 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 334 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7073 (mtm180) cc_final: 0.6262 (pmt-80) REVERT: D 204 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7837 (m) REVERT: G 472 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: G 535 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6731 (pp20) REVERT: J 214 LYS cc_start: 0.8422 (mtpt) cc_final: 0.7969 (mtpt) REVERT: M 602 ASN cc_start: 0.6970 (t0) cc_final: 0.6734 (t0) REVERT: P 185 ASP cc_start: 0.7814 (m-30) cc_final: 0.7444 (m-30) REVERT: P 449 ARG cc_start: 0.7076 (mtm180) cc_final: 0.6328 (pmt-80) REVERT: P 535 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: P 579 ASP cc_start: 0.7699 (t0) cc_final: 0.7479 (t0) REVERT: P 602 ASN cc_start: 0.6576 (t0) cc_final: 0.6295 (t0) REVERT: R 70 LEU cc_start: 0.8523 (mt) cc_final: 0.8114 (mt) REVERT: S 449 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6334 (pmt-80) REVERT: S 535 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7063 (pp20) REVERT: S 541 GLN cc_start: 0.8579 (mt0) cc_final: 0.8317 (mt0) outliers start: 80 outliers final: 66 residues processed: 387 average time/residue: 0.4519 time to fit residues: 268.6283 Evaluate side-chains 394 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 323 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 194 VAL Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 535 GLU Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 0.0970 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 248 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 286 optimal weight: 0.0570 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** 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 561 ASN ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29078 Z= 0.186 Angle : 0.483 7.116 39606 Z= 0.251 Chirality : 0.043 0.197 4501 Planarity : 0.004 0.059 5180 Dihedral : 3.790 20.459 4102 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.63 % Allowed : 13.46 % Favored : 83.91 % 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: -0.66 (0.13), residues: 3745 helix: 0.13 (0.25), residues: 504 sheet: 0.55 (0.17), residues: 882 loop : -0.99 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 35 HIS 0.006 0.001 HIS G 263 PHE 0.017 0.001 PHE R 64 TYR 0.021 0.001 TYR U 52 ARG 0.002 0.000 ARG J 297 *********************** REFINEMENT MACRO_CYCLE 8 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 404 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 331 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6240 (pmt-80) REVERT: D 204 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7826 (m) REVERT: D 535 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: G 472 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: G 535 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: J 214 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7975 (mtpt) REVERT: P 185 ASP cc_start: 0.7779 (m-30) cc_final: 0.7400 (m-30) REVERT: P 449 ARG cc_start: 0.7073 (mtm180) cc_final: 0.6327 (pmt-80) REVERT: P 535 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7283 (pp20) REVERT: P 579 ASP cc_start: 0.7698 (t0) cc_final: 0.7482 (t0) REVERT: P 602 ASN cc_start: 0.6566 (t0) cc_final: 0.6303 (t0) REVERT: R 70 LEU cc_start: 0.8512 (mt) cc_final: 0.8115 (mt) REVERT: S 449 ARG cc_start: 0.6847 (mtm180) cc_final: 0.6309 (pmt-80) REVERT: S 535 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7127 (pp20) REVERT: S 541 GLN cc_start: 0.8587 (mt0) cc_final: 0.8296 (mt0) outliers start: 73 outliers final: 64 residues processed: 379 average time/residue: 0.4553 time to fit residues: 264.8486 Evaluate side-chains 394 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 324 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 535 GLU Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain U residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.6980 chunk 349 optimal weight: 0.0870 chunk 318 optimal weight: 1.9990 chunk 339 optimal weight: 0.0980 chunk 348 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 HIS ** J 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 602 ASN Q 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29078 Z= 0.197 Angle : 0.495 7.647 39606 Z= 0.257 Chirality : 0.043 0.218 4501 Planarity : 0.004 0.061 5180 Dihedral : 3.822 20.634 4102 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.78 % Allowed : 13.67 % Favored : 83.55 % 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: -0.67 (0.13), residues: 3745 helix: 0.12 (0.25), residues: 504 sheet: 0.63 (0.17), residues: 868 loop : -1.03 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 35 HIS 0.006 0.001 HIS P 263 PHE 0.018 0.001 PHE R 64 TYR 0.017 0.001 TYR U 52 ARG 0.003 0.000 ARG P 297 *********************** REFINEMENT MACRO_CYCLE 9 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 399 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 322 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6334 (pmt-80) REVERT: D 204 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7834 (m) REVERT: F 31 ASN cc_start: 0.8050 (t0) cc_final: 0.7326 (m-40) REVERT: G 472 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: G 535 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: J 214 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7935 (mtpt) REVERT: M 297 ARG cc_start: 0.7015 (mtp180) cc_final: 0.6761 (mtp85) REVERT: P 185 ASP cc_start: 0.7791 (m-30) cc_final: 0.7409 (m-30) REVERT: P 449 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6334 (pmt-80) REVERT: P 535 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: P 579 ASP cc_start: 0.7696 (t0) cc_final: 0.7468 (t0) REVERT: R 70 LEU cc_start: 0.8527 (mt) cc_final: 0.8098 (mt) REVERT: S 449 ARG cc_start: 0.6864 (mtm180) cc_final: 0.6325 (pmt-80) REVERT: S 541 GLN cc_start: 0.8591 (mt0) cc_final: 0.8292 (mt0) outliers start: 77 outliers final: 64 residues processed: 371 average time/residue: 0.4552 time to fit residues: 262.3493 Evaluate side-chains 382 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 314 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain P residue 587 MET Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.1980 chunk 222 optimal weight: 0.7980 chunk 359 optimal weight: 5.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 376 optimal weight: 10.0000 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 231 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 561 ASN ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29078 Z= 0.241 Angle : 0.520 7.964 39606 Z= 0.269 Chirality : 0.044 0.263 4501 Planarity : 0.005 0.063 5180 Dihedral : 3.975 21.389 4102 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.60 % Allowed : 13.85 % Favored : 83.55 % 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: -0.79 (0.13), residues: 3745 helix: 0.00 (0.25), residues: 504 sheet: 0.42 (0.17), residues: 903 loop : -1.06 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 35 HIS 0.008 0.001 HIS J 263 PHE 0.019 0.001 PHE R 64 TYR 0.016 0.001 TYR U 52 ARG 0.003 0.000 ARG P 592 ********************** REFINEMENT MACRO_CYCLE 10 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 398 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 326 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6448 (pmt-80) REVERT: B 52 SER cc_start: 0.7969 (t) cc_final: 0.7541 (t) REVERT: D 204 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7852 (m) REVERT: F 31 ASN cc_start: 0.8068 (t0) cc_final: 0.7321 (m-40) REVERT: G 472 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: G 535 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6697 (pp20) REVERT: J 214 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7940 (mtpt) REVERT: M 297 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6731 (mtp85) REVERT: P 185 ASP cc_start: 0.7830 (m-30) cc_final: 0.7444 (m-30) REVERT: P 449 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6338 (pmt-80) REVERT: P 535 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: P 579 ASP cc_start: 0.7721 (t0) cc_final: 0.7498 (t0) REVERT: R 70 LEU cc_start: 0.8595 (mt) cc_final: 0.8174 (mt) REVERT: S 449 ARG cc_start: 0.6972 (mtm180) cc_final: 0.6375 (pmt-80) REVERT: S 541 GLN cc_start: 0.8618 (mt0) cc_final: 0.8298 (mt0) outliers start: 72 outliers final: 63 residues processed: 371 average time/residue: 0.4526 time to fit residues: 256.0620 Evaluate side-chains 387 residues out of total 2772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 320 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain G residue 535 GLU Chi-restraints excluded: chain G residue 587 MET Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain J residue 185 ASP Chi-restraints excluded: chain J residue 194 VAL Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 332 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 374 ILE Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain J residue 587 MET Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain M residue 185 ASP Chi-restraints excluded: chain M residue 194 VAL Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 213 LYS Chi-restraints excluded: chain M residue 367 VAL Chi-restraints excluded: chain M residue 374 ILE Chi-restraints excluded: chain M residue 404 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain N residue 53 ARG Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 210 ILE Chi-restraints excluded: chain P residue 367 VAL Chi-restraints excluded: chain P residue 374 ILE Chi-restraints excluded: chain P residue 404 ILE Chi-restraints excluded: chain P residue 469 VAL Chi-restraints excluded: chain P residue 535 GLU Chi-restraints excluded: chain Q residue 53 ARG Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 185 ASP Chi-restraints excluded: chain S residue 210 ILE Chi-restraints excluded: chain S residue 367 VAL Chi-restraints excluded: chain S residue 374 ILE Chi-restraints excluded: chain S residue 587 MET Chi-restraints excluded: chain U residue 30 THR Chi-restraints excluded: chain U residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 319 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 276 optimal weight: 0.3980 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 300 optimal weight: 0.0370 chunk 125 optimal weight: 2.9990 chunk 308 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** M 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.190210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140939 restraints weight = 36148.455| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.49 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29078 Z= 0.196 Angle : 0.501 7.354 39606 Z= 0.260 Chirality : 0.043 0.216 4501 Planarity : 0.004 0.061 5180 Dihedral : 3.884 21.377 4102 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.45 % Allowed : 14.32 % Favored : 83.23 % 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: -0.73 (0.13), residues: 3745 helix: 0.07 (0.25), residues: 504 sheet: 0.54 (0.17), residues: 889 loop : -1.05 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 35 HIS 0.009 0.001 HIS J 263 PHE 0.019 0.001 PHE R 64 TYR 0.016 0.001 TYR U 52 ARG 0.008 0.000 ARG G 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6177.35 seconds wall clock time: 114 minutes 1.20 seconds (6841.20 seconds total)