Starting phenix.real_space_refine on Fri Mar 22 21:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/03_2024/7rlh_24530_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/03_2024/7rlh_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_24530/03_2024/7rlh_24530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/03_2024/7rlh_24530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/03_2024/7rlh_24530_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rlh_24530/03_2024/7rlh_24530_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 688} 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: 17.56, per 1000 atoms: 0.51 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: 13.90 Conformation dependent library (CDL) restraints added in 6.7 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: 8.65 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: 13.60 Time building geometry restraints manager: 15.08 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: 19864 16.75 - 33.49: 1482 33.49 - 50.24: 386 50.24 - 66.98: 48 66.98 - 83.73: 54 Dihedral angle restraints: 21834 sinusoidal: 9264 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 21831 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 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.020 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 95.280 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 13.638 83.727 13686 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 % Allowed : 0.16 % Favored : 99.84 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 551 HIS 0.007 0.001 HIS D 317 PHE 0.013 0.002 PHE D 267 TYR 0.018 0.002 TYR E 173 ARG 0.009 0.001 ARG C 113 *********************** 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 : 4.165 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.9082 (mm) cc_final: 0.8879 (mm) REVERT: B 275 MET cc_start: 0.9203 (mmm) cc_final: 0.8989 (mmm) REVERT: C 143 TYR cc_start: 0.8913 (m-80) cc_final: 0.8125 (m-10) REVERT: D 275 MET cc_start: 0.9224 (mmm) cc_final: 0.8981 (mmm) REVERT: E 63 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8115 (tptp) REVERT: F 59 LEU cc_start: 0.9092 (mm) cc_final: 0.8879 (mm) REVERT: F 450 ASP cc_start: 0.8716 (t0) cc_final: 0.8516 (t0) outliers start: 0 outliers final: 2 residues processed: 303 average time/residue: 1.7375 time to fit residues: 615.1718 Evaluate side-chains 178 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain F residue 508 MET 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** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35154 Z= 0.302 Angle : 0.603 7.868 47556 Z= 0.302 Chirality : 0.045 0.139 5364 Planarity : 0.005 0.053 6234 Dihedral : 8.247 53.097 4986 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.26 % Favored : 95.47 % Rotamer: Outliers : 1.24 % Allowed : 6.09 % Favored : 92.68 % 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: 0.44 (0.13), residues: 4344 helix: 1.19 (0.13), residues: 1878 sheet: 0.12 (0.21), residues: 594 loop : -0.51 (0.16), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 551 HIS 0.005 0.001 HIS F 317 PHE 0.029 0.002 PHE E 139 TYR 0.010 0.002 TYR E 203 ARG 0.011 0.001 ARG B 155 *********************** 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 243 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 197 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7740 (tpt) cc_final: 0.7520 (tpt) REVERT: A 134 TYR cc_start: 0.8824 (m-80) cc_final: 0.8524 (m-10) REVERT: A 508 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4032 (mpt) REVERT: B 84 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7504 (tpt) REVERT: B 427 MET cc_start: 0.7541 (tpt) cc_final: 0.7325 (tpt) REVERT: B 561 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: C 84 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7234 (tpt) REVERT: C 143 TYR cc_start: 0.8913 (m-80) cc_final: 0.8233 (m-10) REVERT: E 63 LYS cc_start: 0.8549 (mtmt) cc_final: 0.8015 (tptp) REVERT: E 84 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7304 (tpt) REVERT: E 139 PHE cc_start: 0.8818 (m-80) cc_final: 0.8416 (m-80) REVERT: F 84 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7199 (tpt) REVERT: F 139 PHE cc_start: 0.9134 (m-10) cc_final: 0.8405 (m-80) REVERT: F 143 TYR cc_start: 0.8949 (m-80) cc_final: 0.8256 (m-10) REVERT: F 450 ASP cc_start: 0.8748 (t0) cc_final: 0.8448 (t0) outliers start: 46 outliers final: 13 residues processed: 218 average time/residue: 1.3615 time to fit residues: 364.2822 Evaluate side-chains 191 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 424 optimal weight: 0.0980 chunk 350 optimal weight: 0.0770 chunk 389 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 315 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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** B 602 ASN ** 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** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35154 Z= 0.148 Angle : 0.517 9.850 47556 Z= 0.259 Chirality : 0.043 0.176 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.797 54.342 4986 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.47 % Favored : 95.26 % Rotamer: Outliers : 0.97 % Allowed : 7.97 % Favored : 91.06 % 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: 1.30 (0.13), residues: 1842 sheet: 0.02 (0.21), residues: 594 loop : -0.44 (0.16), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 551 HIS 0.003 0.000 HIS F 317 PHE 0.017 0.001 PHE E 139 TYR 0.011 0.001 TYR D 110 ARG 0.010 0.000 ARG E 323 *********************** 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 224 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7834 (tpt) cc_final: 0.7610 (tpt) REVERT: A 508 MET cc_start: 0.5170 (OUTLIER) cc_final: 0.4070 (mpt) REVERT: A 561 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: B 84 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7656 (tpt) REVERT: B 442 MET cc_start: 0.9288 (tpp) cc_final: 0.8866 (mpp) REVERT: B 561 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: C 84 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7508 (tpt) REVERT: C 139 PHE cc_start: 0.9102 (m-80) cc_final: 0.8881 (m-80) REVERT: C 143 TYR cc_start: 0.8915 (m-80) cc_final: 0.8338 (m-10) REVERT: C 449 MET cc_start: 0.8980 (tpt) cc_final: 0.8716 (tpp) REVERT: D 158 MET cc_start: 0.8633 (mtp) cc_final: 0.8424 (ttp) REVERT: D 508 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.3897 (mpt) REVERT: D 561 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7784 (pt0) REVERT: E 63 LYS cc_start: 0.8534 (mtmt) cc_final: 0.7995 (tptp) REVERT: E 84 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: E 139 PHE cc_start: 0.8694 (m-80) cc_final: 0.8343 (m-80) REVERT: E 158 MET cc_start: 0.8712 (ttm) cc_final: 0.8343 (tmt) REVERT: E 449 MET cc_start: 0.8912 (tpp) cc_final: 0.8261 (tpp) REVERT: E 561 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: F 84 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7628 (tpt) REVERT: F 143 TYR cc_start: 0.8903 (m-80) cc_final: 0.8259 (m-10) REVERT: F 450 ASP cc_start: 0.8701 (t0) cc_final: 0.8437 (t0) REVERT: F 508 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.4137 (mpt) outliers start: 36 outliers final: 12 residues processed: 210 average time/residue: 1.3351 time to fit residues: 344.0764 Evaluate side-chains 190 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 442 MET Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 0.0060 chunk 295 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 394 optimal weight: 0.5980 chunk 417 optimal weight: 0.7980 chunk 206 optimal weight: 0.1980 chunk 373 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 ** E 36 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1694 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= 0.186 Angle : 0.506 7.248 47556 Z= 0.254 Chirality : 0.043 0.178 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.647 57.789 4986 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.07 % Favored : 95.65 % Rotamer: Outliers : 1.48 % Allowed : 9.07 % Favored : 89.45 % 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: 0.63 (0.14), residues: 4344 helix: 1.40 (0.13), residues: 1842 sheet: 0.20 (0.21), residues: 582 loop : -0.41 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 476 HIS 0.003 0.001 HIS F 317 PHE 0.012 0.001 PHE A 552 TYR 0.011 0.001 TYR F 203 ARG 0.006 0.000 ARG B 155 *********************** 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 233 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 4.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7880 (tpt) cc_final: 0.7501 (tmm) REVERT: A 169 ASP cc_start: 0.3163 (OUTLIER) cc_final: 0.2524 (p0) REVERT: A 508 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4085 (mpt) REVERT: A 561 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7903 (pt0) REVERT: B 101 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8764 (p) REVERT: B 169 ASP cc_start: 0.2634 (OUTLIER) cc_final: 0.2071 (p0) REVERT: B 442 MET cc_start: 0.9296 (tpp) cc_final: 0.8915 (mpp) REVERT: B 449 MET cc_start: 0.8953 (tpp) cc_final: 0.8333 (tpp) REVERT: B 508 MET cc_start: 0.5346 (mmt) cc_final: 0.4603 (mmt) REVERT: B 534 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: B 561 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: B 742 PHE cc_start: 0.8485 (m-80) cc_final: 0.8264 (m-10) REVERT: C 84 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7706 (tpt) REVERT: C 139 PHE cc_start: 0.9162 (m-80) cc_final: 0.8792 (m-80) REVERT: C 143 TYR cc_start: 0.8917 (m-80) cc_final: 0.8389 (m-10) REVERT: C 155 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8202 (mtt-85) REVERT: C 169 ASP cc_start: 0.2085 (OUTLIER) cc_final: 0.1756 (p0) REVERT: C 219 MET cc_start: 0.8520 (mtm) cc_final: 0.8277 (ptp) REVERT: C 449 MET cc_start: 0.8987 (tpt) cc_final: 0.8703 (tpp) REVERT: D 36 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7172 (t0) REVERT: D 169 ASP cc_start: 0.2899 (OUTLIER) cc_final: 0.2416 (p0) REVERT: D 508 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.3931 (mpt) REVERT: D 561 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: E 63 LYS cc_start: 0.8538 (mtmt) cc_final: 0.8010 (tptp) REVERT: E 84 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7559 (tpt) REVERT: E 101 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8788 (p) REVERT: E 139 PHE cc_start: 0.8762 (m-80) cc_final: 0.8343 (m-80) REVERT: E 169 ASP cc_start: 0.2614 (OUTLIER) cc_final: 0.2018 (p0) REVERT: E 561 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: F 84 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7769 (tpt) REVERT: F 139 PHE cc_start: 0.9089 (m-10) cc_final: 0.8226 (m-80) REVERT: F 143 TYR cc_start: 0.8936 (m-80) cc_final: 0.8372 (m-10) REVERT: F 169 ASP cc_start: 0.2217 (OUTLIER) cc_final: 0.1881 (p0) REVERT: F 450 ASP cc_start: 0.8767 (t0) cc_final: 0.8476 (t0) REVERT: F 508 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.4131 (mpt) outliers start: 55 outliers final: 18 residues processed: 217 average time/residue: 1.2827 time to fit residues: 344.3784 Evaluate side-chains 205 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 4.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 534 GLU Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 374 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** C 36 ASN ** 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 406 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 HIS F 36 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35154 Z= 0.301 Angle : 0.544 7.327 47556 Z= 0.275 Chirality : 0.045 0.172 5364 Planarity : 0.004 0.057 6234 Dihedral : 7.821 58.963 4986 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.30 % Favored : 95.42 % Rotamer: Outliers : 1.80 % Allowed : 10.04 % Favored : 88.15 % 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: 0.64 (0.14), residues: 4344 helix: 1.36 (0.13), residues: 1878 sheet: 0.20 (0.21), residues: 612 loop : -0.39 (0.16), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 476 HIS 0.003 0.001 HIS A 384 PHE 0.015 0.002 PHE B 506 TYR 0.012 0.002 TYR B 138 ARG 0.009 0.001 ARG A 766 *********************** 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 246 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 179 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.3229 (OUTLIER) cc_final: 0.2486 (p0) REVERT: A 508 MET cc_start: 0.5105 (OUTLIER) cc_final: 0.4126 (mpt) REVERT: A 561 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 36 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7275 (t0) REVERT: B 101 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8806 (p) REVERT: B 158 MET cc_start: 0.9145 (ptp) cc_final: 0.8932 (ptm) REVERT: B 169 ASP cc_start: 0.2720 (OUTLIER) cc_final: 0.2152 (p0) REVERT: B 449 MET cc_start: 0.8950 (tpp) cc_final: 0.8214 (tpp) REVERT: B 508 MET cc_start: 0.5180 (mmt) cc_final: 0.4573 (mmt) REVERT: B 561 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: B 586 ARG cc_start: 0.3339 (mtt-85) cc_final: 0.3137 (mtp85) REVERT: C 139 PHE cc_start: 0.9138 (m-80) cc_final: 0.8764 (m-80) REVERT: C 169 ASP cc_start: 0.2200 (OUTLIER) cc_final: 0.1779 (p0) REVERT: C 449 MET cc_start: 0.8982 (tpt) cc_final: 0.8701 (tpp) REVERT: D 169 ASP cc_start: 0.3036 (OUTLIER) cc_final: 0.2427 (p0) REVERT: D 508 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.5085 (mpt) REVERT: D 561 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (pt0) REVERT: E 63 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8018 (tptp) REVERT: E 101 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8795 (p) REVERT: E 139 PHE cc_start: 0.8758 (m-80) cc_final: 0.8338 (m-80) REVERT: E 169 ASP cc_start: 0.2741 (OUTLIER) cc_final: 0.2119 (p0) REVERT: E 442 MET cc_start: 0.9389 (tpp) cc_final: 0.9117 (mpp) REVERT: E 561 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: F 36 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.7068 (t0) REVERT: F 84 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7707 (tpt) REVERT: F 139 PHE cc_start: 0.9043 (m-10) cc_final: 0.8247 (m-80) REVERT: F 143 TYR cc_start: 0.8930 (m-80) cc_final: 0.8302 (m-10) REVERT: F 169 ASP cc_start: 0.2224 (OUTLIER) cc_final: 0.1822 (p0) REVERT: F 450 ASP cc_start: 0.8780 (t0) cc_final: 0.8502 (t0) REVERT: F 508 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.4135 (mpt) outliers start: 67 outliers final: 26 residues processed: 233 average time/residue: 1.2829 time to fit residues: 372.5652 Evaluate side-chains 212 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 580 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.0980 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 103 optimal weight: 0.0020 chunk 417 optimal weight: 8.9990 chunk 346 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 219 optimal weight: 30.0000 overall best weight: 1.2192 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN D 36 ASN ** E 36 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2019 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= 0.194 Angle : 0.523 9.338 47556 Z= 0.261 Chirality : 0.043 0.179 5364 Planarity : 0.004 0.054 6234 Dihedral : 7.732 59.888 4986 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.10 % Favored : 95.63 % Rotamer: Outliers : 1.59 % Allowed : 11.28 % Favored : 87.13 % 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: 0.69 (0.14), residues: 4344 helix: 1.43 (0.13), residues: 1848 sheet: 0.27 (0.21), residues: 588 loop : -0.38 (0.16), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 476 HIS 0.002 0.001 HIS B 317 PHE 0.012 0.001 PHE F 552 TYR 0.008 0.001 TYR D 134 ARG 0.005 0.000 ARG D 766 *********************** 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 235 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 176 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.8488 (ttp) cc_final: 0.8136 (pp-130) REVERT: A 169 ASP cc_start: 0.2874 (OUTLIER) cc_final: 0.2206 (p0) REVERT: A 561 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: B 101 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (p) REVERT: B 158 MET cc_start: 0.9040 (ptp) cc_final: 0.8813 (ptm) REVERT: B 169 ASP cc_start: 0.2709 (OUTLIER) cc_final: 0.2120 (p0) REVERT: B 442 MET cc_start: 0.9321 (tpp) cc_final: 0.9044 (mpp) REVERT: B 449 MET cc_start: 0.8948 (tpp) cc_final: 0.8227 (tpp) REVERT: B 561 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: C 139 PHE cc_start: 0.9149 (m-80) cc_final: 0.8668 (m-80) REVERT: C 169 ASP cc_start: 0.2031 (OUTLIER) cc_final: 0.1605 (p0) REVERT: C 449 MET cc_start: 0.8989 (tpt) cc_final: 0.8710 (tpp) REVERT: D 169 ASP cc_start: 0.2876 (OUTLIER) cc_final: 0.2337 (p0) REVERT: D 508 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.5076 (mpt) REVERT: D 561 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7920 (pt0) REVERT: E 63 LYS cc_start: 0.8518 (mtmt) cc_final: 0.7991 (tptp) REVERT: E 101 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8755 (p) REVERT: E 139 PHE cc_start: 0.8769 (m-80) cc_final: 0.8310 (m-80) REVERT: E 169 ASP cc_start: 0.2675 (OUTLIER) cc_final: 0.1990 (p0) REVERT: E 442 MET cc_start: 0.9359 (tpp) cc_final: 0.9077 (mpp) REVERT: E 449 MET cc_start: 0.8887 (tpp) cc_final: 0.8318 (tpp) REVERT: E 508 MET cc_start: 0.5455 (mmt) cc_final: 0.4636 (mmt) REVERT: E 561 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: F 135 LEU cc_start: 0.9189 (mp) cc_final: 0.8792 (mp) REVERT: F 139 PHE cc_start: 0.9075 (m-10) cc_final: 0.8204 (m-80) REVERT: F 143 TYR cc_start: 0.8929 (m-80) cc_final: 0.8374 (m-10) REVERT: F 169 ASP cc_start: 0.2433 (OUTLIER) cc_final: 0.1943 (p0) REVERT: F 450 ASP cc_start: 0.8774 (t0) cc_final: 0.8517 (OUTLIER) outliers start: 59 outliers final: 35 residues processed: 225 average time/residue: 1.2193 time to fit residues: 342.4897 Evaluate side-chains 216 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 238 optimal weight: 0.0870 chunk 305 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 351 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 416 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 602 ASN E 36 ASN E 90 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 35154 Z= 0.159 Angle : 0.499 9.810 47556 Z= 0.249 Chirality : 0.042 0.156 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.556 59.902 4986 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 1.59 % Allowed : 11.66 % Favored : 86.75 % 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: 1.53 (0.13), residues: 1842 sheet: 0.26 (0.21), residues: 588 loop : -0.32 (0.16), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 476 HIS 0.002 0.000 HIS B 317 PHE 0.021 0.001 PHE B 742 TYR 0.011 0.001 TYR B 138 ARG 0.005 0.000 ARG D 766 *********************** 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 242 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 4.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9004 (m-80) cc_final: 0.8663 (m-10) REVERT: A 169 ASP cc_start: 0.2831 (OUTLIER) cc_final: 0.2106 (p0) REVERT: A 449 MET cc_start: 0.8808 (tpp) cc_final: 0.8316 (tpp) REVERT: A 561 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7932 (pt0) REVERT: B 36 ASN cc_start: 0.7802 (OUTLIER) cc_final: 0.7349 (t160) REVERT: B 101 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 169 ASP cc_start: 0.2599 (OUTLIER) cc_final: 0.1940 (p0) REVERT: B 442 MET cc_start: 0.9338 (tpp) cc_final: 0.9049 (mpp) REVERT: B 449 MET cc_start: 0.8965 (tpp) cc_final: 0.8187 (tpp) REVERT: B 561 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: C 36 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6949 (t0) REVERT: C 139 PHE cc_start: 0.9143 (m-80) cc_final: 0.8674 (m-80) REVERT: C 155 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8108 (mtp85) REVERT: C 169 ASP cc_start: 0.2410 (OUTLIER) cc_final: 0.1999 (p0) REVERT: C 449 MET cc_start: 0.8988 (tpt) cc_final: 0.8715 (tpp) REVERT: D 169 ASP cc_start: 0.2764 (OUTLIER) cc_final: 0.2198 (p0) REVERT: D 450 ASP cc_start: 0.8823 (t0) cc_final: 0.8585 (t0) REVERT: D 508 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.3973 (mpt) REVERT: D 561 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: E 36 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7346 (t0) REVERT: E 63 LYS cc_start: 0.8520 (mtmt) cc_final: 0.8049 (tptp) REVERT: E 139 PHE cc_start: 0.8772 (m-80) cc_final: 0.8358 (m-80) REVERT: E 169 ASP cc_start: 0.2469 (OUTLIER) cc_final: 0.1845 (p0) REVERT: E 442 MET cc_start: 0.9366 (tpp) cc_final: 0.9084 (mpp) REVERT: E 449 MET cc_start: 0.8930 (tpp) cc_final: 0.8269 (tpp) REVERT: E 508 MET cc_start: 0.5362 (mmt) cc_final: 0.4802 (mmt) REVERT: E 561 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: F 135 LEU cc_start: 0.9188 (mp) cc_final: 0.8814 (mp) REVERT: F 139 PHE cc_start: 0.9063 (m-10) cc_final: 0.8224 (m-80) REVERT: F 143 TYR cc_start: 0.8939 (m-80) cc_final: 0.8343 (m-10) REVERT: F 169 ASP cc_start: 0.2286 (OUTLIER) cc_final: 0.1757 (p0) REVERT: F 449 MET cc_start: 0.8819 (tpp) cc_final: 0.8440 (tpp) REVERT: F 450 ASP cc_start: 0.8763 (t0) cc_final: 0.8479 (t0) outliers start: 59 outliers final: 34 residues processed: 235 average time/residue: 1.2228 time to fit residues: 357.6465 Evaluate side-chains 218 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE 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: 0.5980 chunk 248 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 264 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 327 optimal weight: 8.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** 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** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35154 Z= 0.328 Angle : 0.580 10.422 47556 Z= 0.289 Chirality : 0.045 0.191 5364 Planarity : 0.005 0.070 6234 Dihedral : 7.788 59.547 4986 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.49 % Favored : 95.23 % Rotamer: Outliers : 1.48 % Allowed : 12.49 % Favored : 86.03 % 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: 0.75 (0.14), residues: 4344 helix: 1.46 (0.13), residues: 1872 sheet: 0.30 (0.21), residues: 606 loop : -0.35 (0.16), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 551 HIS 0.003 0.001 HIS C 384 PHE 0.018 0.002 PHE B 506 TYR 0.011 0.001 TYR E 138 ARG 0.011 0.001 ARG A 766 *********************** 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 237 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 182 time to evaluate : 4.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9080 (m-80) cc_final: 0.8731 (m-10) REVERT: A 158 MET cc_start: 0.8502 (ttp) cc_final: 0.8192 (pp-130) REVERT: A 169 ASP cc_start: 0.3008 (OUTLIER) cc_final: 0.2287 (p0) REVERT: A 449 MET cc_start: 0.8901 (tpp) cc_final: 0.8155 (tpp) REVERT: A 561 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: B 101 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8788 (p) REVERT: B 169 ASP cc_start: 0.2583 (OUTLIER) cc_final: 0.1899 (p0) REVERT: B 442 MET cc_start: 0.9372 (tpp) cc_final: 0.9078 (mpp) REVERT: B 561 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: B 586 ARG cc_start: 0.3335 (mtt-85) cc_final: 0.3130 (mtp85) REVERT: C 139 PHE cc_start: 0.9149 (m-80) cc_final: 0.8718 (m-80) REVERT: C 169 ASP cc_start: 0.2310 (OUTLIER) cc_final: 0.1887 (p0) REVERT: C 449 MET cc_start: 0.9001 (tpt) cc_final: 0.8711 (tpp) REVERT: D 62 LYS cc_start: 0.9081 (mmpt) cc_final: 0.8804 (mmpt) REVERT: D 169 ASP cc_start: 0.2855 (OUTLIER) cc_final: 0.2312 (p0) REVERT: D 449 MET cc_start: 0.8867 (tpp) cc_final: 0.8244 (tpp) REVERT: D 508 MET cc_start: 0.5216 (OUTLIER) cc_final: 0.4087 (mpt) REVERT: D 561 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8008 (pt0) REVERT: E 63 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8086 (tptp) REVERT: E 139 PHE cc_start: 0.8794 (m-80) cc_final: 0.8411 (m-80) REVERT: E 169 ASP cc_start: 0.2625 (OUTLIER) cc_final: 0.1938 (p0) REVERT: E 442 MET cc_start: 0.9413 (tpp) cc_final: 0.9121 (mpp) REVERT: E 449 MET cc_start: 0.8970 (tpp) cc_final: 0.8179 (tpp) REVERT: E 561 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8015 (pt0) REVERT: F 139 PHE cc_start: 0.9066 (m-10) cc_final: 0.8328 (m-80) REVERT: F 143 TYR cc_start: 0.8956 (m-80) cc_final: 0.8360 (m-10) REVERT: F 169 ASP cc_start: 0.2293 (OUTLIER) cc_final: 0.1766 (p0) REVERT: F 508 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.4202 (mpt) outliers start: 55 outliers final: 36 residues processed: 229 average time/residue: 1.2658 time to fit residues: 359.6028 Evaluate side-chains 219 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 170 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE 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: 10.0000 chunk 363 optimal weight: 30.0000 chunk 388 optimal weight: 0.9990 chunk 233 optimal weight: 0.0000 chunk 169 optimal weight: 0.8980 chunk 304 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 350 optimal weight: 0.7980 chunk 366 optimal weight: 6.9990 chunk 386 optimal weight: 4.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 A 602 ASN ** 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** ** 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 558 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2342 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= 0.167 Angle : 0.536 12.264 47556 Z= 0.264 Chirality : 0.043 0.206 5364 Planarity : 0.004 0.055 6234 Dihedral : 7.637 58.896 4986 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.44 % Favored : 95.28 % Rotamer: Outliers : 1.48 % Allowed : 12.98 % Favored : 85.54 % 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: 0.78 (0.14), residues: 4344 helix: 1.53 (0.13), residues: 1836 sheet: 0.26 (0.22), residues: 588 loop : -0.33 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 551 HIS 0.002 0.000 HIS B 317 PHE 0.022 0.001 PHE B 742 TYR 0.010 0.001 TYR D 134 ARG 0.005 0.000 ARG D 766 *********************** 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 238 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9053 (m-80) cc_final: 0.8734 (m-10) REVERT: A 158 MET cc_start: 0.8512 (ttp) cc_final: 0.8121 (pp-130) REVERT: A 169 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.2315 (p0) REVERT: A 449 MET cc_start: 0.8903 (tpp) cc_final: 0.8124 (tpp) REVERT: A 561 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: B 101 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8804 (p) REVERT: B 169 ASP cc_start: 0.2487 (OUTLIER) cc_final: 0.1836 (p0) REVERT: B 442 MET cc_start: 0.9350 (tpp) cc_final: 0.9043 (mpp) REVERT: B 508 MET cc_start: 0.5376 (mmt) cc_final: 0.4814 (mmt) REVERT: B 561 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: C 139 PHE cc_start: 0.9152 (m-80) cc_final: 0.8677 (m-80) REVERT: C 169 ASP cc_start: 0.2224 (OUTLIER) cc_final: 0.1809 (p0) REVERT: C 449 MET cc_start: 0.9005 (tpt) cc_final: 0.8722 (tpp) REVERT: D 62 LYS cc_start: 0.9061 (mmpt) cc_final: 0.8790 (mmpt) REVERT: D 169 ASP cc_start: 0.2639 (OUTLIER) cc_final: 0.2102 (p0) REVERT: D 449 MET cc_start: 0.8892 (tpp) cc_final: 0.8135 (tpp) REVERT: D 508 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.3928 (mpt) REVERT: D 561 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: E 63 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8085 (tptp) REVERT: E 139 PHE cc_start: 0.8809 (m-80) cc_final: 0.8413 (m-80) REVERT: E 169 ASP cc_start: 0.2504 (OUTLIER) cc_final: 0.1826 (p0) REVERT: E 442 MET cc_start: 0.9384 (tpp) cc_final: 0.9093 (mpp) REVERT: E 449 MET cc_start: 0.8988 (tpp) cc_final: 0.8176 (tpp) REVERT: E 508 MET cc_start: 0.5499 (mmt) cc_final: 0.4810 (mmt) REVERT: E 561 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: E 742 PHE cc_start: 0.8444 (m-80) cc_final: 0.8226 (m-10) REVERT: F 139 PHE cc_start: 0.9107 (m-10) cc_final: 0.8345 (m-80) REVERT: F 143 TYR cc_start: 0.8941 (m-80) cc_final: 0.8360 (m-10) REVERT: F 169 ASP cc_start: 0.2239 (OUTLIER) cc_final: 0.1744 (p0) REVERT: F 449 MET cc_start: 0.8599 (tpp) cc_final: 0.8342 (tpp) REVERT: F 450 ASP cc_start: 0.8718 (t0) cc_final: 0.8404 (t0) outliers start: 55 outliers final: 37 residues processed: 232 average time/residue: 1.1766 time to fit residues: 342.6639 Evaluate side-chains 217 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 4.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE 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: 0.7980 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 285 optimal weight: 0.6980 chunk 430 optimal weight: 6.9990 chunk 396 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 264 optimal weight: 0.4980 chunk 210 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2425 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= 0.166 Angle : 0.533 11.257 47556 Z= 0.263 Chirality : 0.043 0.198 5364 Planarity : 0.004 0.054 6234 Dihedral : 7.531 59.535 4986 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.28 % Favored : 95.44 % Rotamer: Outliers : 1.37 % Allowed : 13.46 % Favored : 85.16 % 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: 0.84 (0.14), residues: 4344 helix: 1.60 (0.13), residues: 1836 sheet: 0.27 (0.22), residues: 588 loop : -0.32 (0.16), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.002 0.001 HIS B 317 PHE 0.013 0.001 PHE B 152 TYR 0.010 0.001 TYR D 134 ARG 0.005 0.000 ARG D 766 ********************** 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: 51 poor density : 168 time to evaluate : 3.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.9095 (m-80) cc_final: 0.8800 (m-10) REVERT: A 169 ASP cc_start: 0.3064 (OUTLIER) cc_final: 0.2321 (p0) REVERT: A 561 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7962 (pt0) REVERT: B 101 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8892 (p) REVERT: B 169 ASP cc_start: 0.2495 (OUTLIER) cc_final: 0.1850 (p0) REVERT: B 442 MET cc_start: 0.9348 (tpp) cc_final: 0.9051 (mpp) REVERT: B 450 ASP cc_start: 0.8688 (t0) cc_final: 0.8389 (OUTLIER) REVERT: B 508 MET cc_start: 0.5246 (mmt) cc_final: 0.4709 (mmt) REVERT: B 561 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: C 139 PHE cc_start: 0.9189 (m-80) cc_final: 0.8701 (m-80) REVERT: C 169 ASP cc_start: 0.2225 (OUTLIER) cc_final: 0.1717 (p0) REVERT: C 449 MET cc_start: 0.9008 (tpt) cc_final: 0.8731 (tpp) REVERT: D 62 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8809 (mmpt) REVERT: D 169 ASP cc_start: 0.2648 (OUTLIER) cc_final: 0.2099 (p0) REVERT: D 508 MET cc_start: 0.5259 (OUTLIER) cc_final: 0.3969 (mpt) REVERT: D 561 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: E 63 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8059 (tptp) REVERT: E 139 PHE cc_start: 0.8850 (m-80) cc_final: 0.8451 (m-80) REVERT: E 158 MET cc_start: 0.8689 (ptm) cc_final: 0.8412 (ppp) REVERT: E 169 ASP cc_start: 0.2406 (OUTLIER) cc_final: 0.1777 (p0) REVERT: E 442 MET cc_start: 0.9379 (tpp) cc_final: 0.9075 (mpp) REVERT: E 508 MET cc_start: 0.5451 (mmt) cc_final: 0.4887 (mmt) REVERT: E 561 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: F 139 PHE cc_start: 0.9089 (m-10) cc_final: 0.8341 (m-80) REVERT: F 143 TYR cc_start: 0.8904 (m-80) cc_final: 0.8324 (m-10) REVERT: F 169 ASP cc_start: 0.2587 (OUTLIER) cc_final: 0.1987 (p0) outliers start: 51 outliers final: 37 residues processed: 213 average time/residue: 1.2616 time to fit residues: 334.8605 Evaluate side-chains 215 residues out of total 3714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 559 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 485 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 561 GLU Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 508 MET Chi-restraints excluded: chain F residue 559 VAL Chi-restraints excluded: chain F residue 580 ASP Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 343 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 352 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 ** 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** C 558 ASN ** 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 ** F 533 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 = 0.3748 r_free = 0.3748 target = 0.101774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.062128 restraints weight = 76897.648| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.12 r_work: 0.2661 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35154 Z= 0.393 Angle : 0.633 12.541 47556 Z= 0.313 Chirality : 0.046 0.187 5364 Planarity : 0.005 0.099 6234 Dihedral : 7.906 59.414 4986 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.67 % Favored : 95.07 % Rotamer: Outliers : 1.51 % Allowed : 13.52 % Favored : 84.98 % 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: 0.64 (0.14), residues: 4344 helix: 1.39 (0.13), residues: 1872 sheet: 0.39 (0.22), residues: 594 loop : -0.49 (0.16), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 551 HIS 0.004 0.001 HIS F 384 PHE 0.023 0.002 PHE B 742 TYR 0.014 0.002 TYR F 134 ARG 0.014 0.001 ARG E 766 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8353.84 seconds wall clock time: 150 minutes 30.04 seconds (9030.04 seconds total)