Starting phenix.real_space_refine (version: dev) on Fri Apr 8 13:37:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/04_2022/7rlh_24530_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.054 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 34584 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "B" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "C" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "D" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "E" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "F" Number of atoms: 5700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5700 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 37, 'TRANS': 688, 'PCIS': 2} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 19.29, per 1000 atoms: 0.56 Number of scatterers: 34584 At special positions: 0 Unit cell: (169, 173, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 36 15.00 Mg 12 11.99 O 6612 8.00 N 6096 7.00 C 21636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.72 Conformation dependent library (CDL) restraints added in 5.2 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 30 sheets defined 40.4% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 removed outlier: 4.037A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.779A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 211 through 225 removed outlier: 5.037A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 427 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.075A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.571A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 568 removed outlier: 3.806A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.037A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.779A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 211 through 225 removed outlier: 5.036A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 427 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.073A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.571A pdb=" N PHE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 removed outlier: 3.807A pdb=" N ARG B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'C' and resid 43 through 48 removed outlier: 4.037A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.778A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 211 through 225 removed outlier: 5.037A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 427 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 removed outlier: 4.075A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.571A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.807A pdb=" N ARG C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.039A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.779A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 211 through 225 removed outlier: 5.037A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 337 through 339 No H-bonds generated for 'chain 'D' and resid 337 through 339' Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 374 through 385 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 427 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.075A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.572A pdb=" N PHE D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 568 removed outlier: 3.807A pdb=" N ARG D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'E' and resid 43 through 48 removed outlier: 4.038A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.779A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 211 through 225 removed outlier: 5.036A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 427 Processing helix chain 'E' and resid 439 through 442 No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.075A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 553 removed outlier: 3.571A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.807A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 583 Processing helix chain 'E' and resid 600 through 609 Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'F' and resid 43 through 48 removed outlier: 4.038A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 removed outlier: 3.780A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 211 through 225 removed outlier: 5.037A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 374 through 385 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 427 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 4.074A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 553 removed outlier: 3.572A pdb=" N PHE F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.807A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 583 Processing helix chain 'F' and resid 600 through 609 Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 760 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.324A pdb=" N ILE A 82 " --> pdb=" O ASP A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 151 through 155 removed outlier: 6.796A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 366 through 368 removed outlier: 6.240A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.524A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= G, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.323A pdb=" N ILE B 82 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 151 through 155 removed outlier: 6.796A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 366 through 368 removed outlier: 6.239A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.524A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 25 through 27 Processing sheet with id= L, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.324A pdb=" N ILE C 82 " --> pdb=" O ASP C 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 151 through 155 removed outlier: 6.797A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 366 through 368 removed outlier: 6.240A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.522A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 Processing sheet with id= Q, first strand: chain 'D' and resid 28 through 30 removed outlier: 6.324A pdb=" N ILE D 82 " --> pdb=" O ASP D 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 151 through 155 removed outlier: 6.796A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 366 through 368 removed outlier: 6.239A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.524A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 25 through 27 Processing sheet with id= V, first strand: chain 'E' and resid 28 through 30 removed outlier: 6.324A pdb=" N ILE E 82 " --> pdb=" O ASP E 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 151 through 155 removed outlier: 6.796A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 366 through 368 removed outlier: 6.240A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.524A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 25 through 27 Processing sheet with id= AA, first strand: chain 'F' and resid 28 through 30 removed outlier: 6.325A pdb=" N ILE F 82 " --> pdb=" O ASP F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'F' and resid 151 through 155 removed outlier: 6.796A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 366 through 368 removed outlier: 6.239A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.524A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) 1056 hydrogen bonds defined for protein. 3150 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: 13.53 Time building geometry restraints manager: 14.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11966 1.37 - 1.51: 10079 1.51 - 1.66: 12809 1.66 - 1.80: 251 1.80 - 1.95: 49 Bond restraints: 35154 Sorted by residual: bond pdb=" CD ARG E 662 " pdb=" NE ARG E 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.49e+00 bond pdb=" CD ARG C 662 " pdb=" NE ARG C 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.45e+00 bond pdb=" CD ARG F 662 " pdb=" NE ARG F 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.39e+00 bond pdb=" CD ARG A 662 " pdb=" NE ARG A 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.38e+00 bond pdb=" CD ARG D 662 " pdb=" NE ARG D 662 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.40e-02 5.10e+03 2.36e+00 ... (remaining 35149 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 1213 106.89 - 113.68: 19894 113.68 - 120.47: 13279 120.47 - 127.26: 12831 127.26 - 134.05: 339 Bond angle restraints: 47556 Sorted by residual: angle pdb=" N TYR B 138 " pdb=" CA TYR B 138 " pdb=" C TYR B 138 " ideal model delta sigma weight residual 114.75 108.88 5.87 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N TYR D 138 " pdb=" CA TYR D 138 " pdb=" C TYR D 138 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.17e+01 angle pdb=" N TYR F 138 " pdb=" CA TYR F 138 " pdb=" C TYR F 138 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.16e+01 angle pdb=" N TYR A 138 " pdb=" CA TYR A 138 " pdb=" C TYR A 138 " ideal model delta sigma weight residual 114.75 108.90 5.85 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N TYR C 138 " pdb=" CA TYR C 138 " pdb=" C TYR C 138 " ideal model delta sigma weight residual 114.75 108.91 5.84 1.26e+00 6.30e-01 2.15e+01 ... (remaining 47551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 19846 16.75 - 33.49: 1422 33.49 - 50.24: 350 50.24 - 66.98: 30 66.98 - 83.73: 54 Dihedral angle restraints: 21702 sinusoidal: 9132 harmonic: 12570 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N PRO B 298 " pdb=" CA PRO B 298 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ALA C 297 " pdb=" C ALA C 297 " pdb=" N PRO C 298 " pdb=" CA PRO C 298 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ALA F 297 " pdb=" C ALA F 297 " pdb=" N PRO F 298 " pdb=" CA PRO F 298 " ideal model delta harmonic sigma weight residual 180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 21699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2915 0.027 - 0.054: 1395 0.054 - 0.081: 585 0.081 - 0.107: 344 0.107 - 0.134: 125 Chirality restraints: 5364 Sorted by residual: chirality pdb=" CA ILE C 371 " pdb=" N ILE C 371 " pdb=" C ILE C 371 " pdb=" CB ILE C 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE F 301 " pdb=" N ILE F 301 " pdb=" C ILE F 301 " pdb=" CB ILE F 301 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 5361 not shown) Planarity restraints: 6234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 297 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 298 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 298 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 298 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 298 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 297 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO E 298 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 298 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 298 " -0.029 5.00e-02 4.00e+02 ... (remaining 6231 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 154 2.41 - 3.03: 21059 3.03 - 3.65: 55156 3.65 - 4.28: 82292 4.28 - 4.90: 132761 Nonbonded interactions: 291422 Sorted by model distance: nonbonded pdb=" OD1 ASP B 478 " pdb=" NH2 ARG B 662 " model vdw 1.783 2.520 nonbonded pdb=" OD1 ASP E 478 " pdb=" NH2 ARG E 662 " model vdw 1.784 2.520 nonbonded pdb=" OD1 ASP C 478 " pdb=" NH2 ARG C 662 " model vdw 1.784 2.520 nonbonded pdb=" OD1 ASP D 478 " pdb=" NH2 ARG D 662 " model vdw 1.784 2.520 nonbonded pdb=" OD1 ASP F 478 " pdb=" NH2 ARG F 662 " model vdw 1.785 2.520 ... (remaining 291417 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 21636 2.51 5 N 6096 2.21 5 O 6612 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.580 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: 0.050 Extract box with map and model: 10.780 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.260 Process input model: 88.320 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.004 0.046 35154 Z= 0.246 Angle : 0.612 8.268 47556 Z= 0.339 Chirality : 0.043 0.134 5364 Planarity : 0.004 0.052 6234 Dihedral : 13.271 83.727 13554 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.05 % Favored : 95.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.36 (0.14), residues: 4344 helix: 1.04 (0.13), residues: 1884 sheet: 0.20 (0.21), residues: 600 loop : -0.49 (0.16), residues: 1860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 4.330 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 303 average time/residue: 1.6327 time to fit residues: 584.2424 Evaluate side-chains 176 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.3420 time to fit residues: 8.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 30.0000 chunk 327 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 220 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 205 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 392 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN F 760 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 35154 Z= 0.302 Angle : 0.598 7.989 47556 Z= 0.300 Chirality : 0.045 0.138 5364 Planarity : 0.005 0.053 6234 Dihedral : 6.624 52.146 4848 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.28 % Favored : 95.44 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.13), residues: 4344 helix: 1.20 (0.13), residues: 1878 sheet: 0.14 (0.21), residues: 594 loop : -0.50 (0.16), residues: 1872 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 11 residues processed: 211 average time/residue: 1.3428 time to fit residues: 351.9410 Evaluate side-chains 178 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 4.398 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.5149 time to fit residues: 9.8464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 424 optimal weight: 0.9980 chunk 350 optimal weight: 0.1980 chunk 389 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 315 optimal weight: 0.0470 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 35154 Z= 0.174 Angle : 0.531 9.603 47556 Z= 0.266 Chirality : 0.043 0.172 5364 Planarity : 0.004 0.054 6234 Dihedral : 6.443 51.304 4848 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.26 % Favored : 95.47 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.51 (0.14), residues: 4344 helix: 1.28 (0.13), residues: 1848 sheet: 0.06 (0.21), residues: 594 loop : -0.44 (0.16), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 4.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 210 average time/residue: 1.2528 time to fit residues: 327.2136 Evaluate side-chains 181 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 1.2938 time to fit residues: 10.0373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 394 optimal weight: 5.9990 chunk 417 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 chunk 373 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 406 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 35154 Z= 0.365 Angle : 0.599 8.414 47556 Z= 0.302 Chirality : 0.046 0.166 5364 Planarity : 0.005 0.072 6234 Dihedral : 6.560 52.564 4848 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.40 % Favored : 95.33 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 4344 helix: 1.25 (0.13), residues: 1884 sheet: 0.13 (0.21), residues: 594 loop : -0.51 (0.16), residues: 1866 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 180 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 227 average time/residue: 1.2367 time to fit residues: 352.6755 Evaluate side-chains 188 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 4.214 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 1.3208 time to fit residues: 7.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 310 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 356 optimal weight: 1.9990 chunk 288 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 35154 Z= 0.217 Angle : 0.538 9.558 47556 Z= 0.270 Chirality : 0.044 0.158 5364 Planarity : 0.004 0.054 6234 Dihedral : 6.457 51.993 4848 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.26 % Favored : 95.47 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.60 (0.14), residues: 4344 helix: 1.35 (0.13), residues: 1878 sheet: 0.12 (0.21), residues: 612 loop : -0.42 (0.16), residues: 1854 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 219 average time/residue: 1.1954 time to fit residues: 331.0751 Evaluate side-chains 193 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 4.205 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 1.2962 time to fit residues: 7.1665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 417 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 35154 Z= 0.433 Angle : 0.630 10.126 47556 Z= 0.316 Chirality : 0.047 0.191 5364 Planarity : 0.005 0.085 6234 Dihedral : 6.624 52.525 4848 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.60 % Favored : 95.12 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.51 (0.14), residues: 4344 helix: 1.27 (0.13), residues: 1866 sheet: 0.30 (0.21), residues: 600 loop : -0.55 (0.16), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 4.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 38 residues processed: 212 average time/residue: 1.1983 time to fit residues: 321.7853 Evaluate side-chains 197 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 4.151 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 37 residues processed: 1 average time/residue: 0.3630 time to fit residues: 6.3915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 6.9990 chunk 47 optimal weight: 0.0770 chunk 238 optimal weight: 0.0060 chunk 305 optimal weight: 0.2980 chunk 236 optimal weight: 0.9990 chunk 351 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 416 optimal weight: 8.9990 chunk 260 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 35154 Z= 0.156 Angle : 0.532 9.360 47556 Z= 0.266 Chirality : 0.043 0.179 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.426 51.872 4848 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.67 % Favored : 95.05 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.14), residues: 4344 helix: 1.45 (0.13), residues: 1824 sheet: 0.19 (0.22), residues: 588 loop : -0.39 (0.16), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 223 average time/residue: 1.2085 time to fit residues: 340.7712 Evaluate side-chains 199 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 1.5423 time to fit residues: 9.5537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 0.4980 chunk 248 optimal weight: 0.5980 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 264 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 35154 Z= 0.195 Angle : 0.542 9.745 47556 Z= 0.269 Chirality : 0.043 0.196 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.349 51.465 4848 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.70 % Favored : 95.05 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 4344 helix: 1.52 (0.13), residues: 1824 sheet: 0.20 (0.21), residues: 612 loop : -0.40 (0.16), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 162 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 39 residues processed: 206 average time/residue: 1.1998 time to fit residues: 311.5076 Evaluate side-chains 195 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 4.234 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 39 residues processed: 0 time to fit residues: 6.1915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 3.9990 chunk 398 optimal weight: 9.9990 chunk 363 optimal weight: 30.0000 chunk 388 optimal weight: 0.7980 chunk 233 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 304 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 350 optimal weight: 0.3980 chunk 366 optimal weight: 2.9990 chunk 386 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 35154 Z= 0.185 Angle : 0.551 11.729 47556 Z= 0.271 Chirality : 0.043 0.196 5364 Planarity : 0.004 0.056 6234 Dihedral : 6.305 51.341 4848 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.70 % Favored : 95.07 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.70 (0.14), residues: 4344 helix: 1.55 (0.13), residues: 1818 sheet: 0.29 (0.21), residues: 594 loop : -0.48 (0.16), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 163 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 40 residues processed: 211 average time/residue: 1.1974 time to fit residues: 319.3373 Evaluate side-chains 198 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 158 time to evaluate : 4.308 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 40 residues processed: 0 time to fit residues: 5.9560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 9.9990 chunk 410 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 chunk 430 optimal weight: 0.6980 chunk 396 optimal weight: 7.9990 chunk 342 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 35154 Z= 0.174 Angle : 0.548 12.312 47556 Z= 0.269 Chirality : 0.043 0.186 5364 Planarity : 0.004 0.055 6234 Dihedral : 6.247 51.286 4848 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.14), residues: 4344 helix: 1.62 (0.13), residues: 1818 sheet: 0.35 (0.22), residues: 576 loop : -0.43 (0.16), residues: 1950 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 44 residues processed: 215 average time/residue: 1.3294 time to fit residues: 366.1662 Evaluate side-chains 200 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 156 time to evaluate : 5.196 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 44 residues processed: 1 average time/residue: 1.6722 time to fit residues: 8.9612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 0.0670 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 533 ASN B 558 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.102490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.063052 restraints weight = 77168.197| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.13 r_work: 0.2857 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work: 0.2824 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work: 0.2807 rms_B_bonded: 2.92 restraints_weight: 0.0625 r_work: 0.2790 rms_B_bonded: 3.01 restraints_weight: 0.0312 r_work: 0.2772 rms_B_bonded: 3.12 restraints_weight: 0.0156 r_work: 0.2753 rms_B_bonded: 3.27 restraints_weight: 0.0078 r_work: 0.2733 rms_B_bonded: 3.44 restraints_weight: 0.0039 r_work: 0.2713 rms_B_bonded: 3.64 restraints_weight: 0.0020 r_work: 0.2691 rms_B_bonded: 3.88 restraints_weight: 0.0010 r_work: 0.2667 rms_B_bonded: 4.15 restraints_weight: 0.0005 r_work: 0.2643 rms_B_bonded: 4.47 restraints_weight: 0.0002 r_work: 0.2617 rms_B_bonded: 4.83 restraints_weight: 0.0001 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 35154 Z= 0.303 Angle : 0.603 13.051 47556 Z= 0.296 Chirality : 0.045 0.201 5364 Planarity : 0.004 0.070 6234 Dihedral : 6.369 52.614 4848 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.37 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 4344 helix: 1.54 (0.13), residues: 1818 sheet: 0.39 (0.22), residues: 594 loop : -0.50 (0.16), residues: 1932 =============================================================================== Job complete usr+sys time: 7239.10 seconds wall clock time: 132 minutes 25.64 seconds (7945.64 seconds total)