Starting phenix.real_space_refine on Sat Mar 16 04:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/03_2024/5irx_8117_trim_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 90 5.16 5 C 8710 2.51 5 N 2098 2.21 5 O 2248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 428": "NH1" <-> "NH2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B ARG 743": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C ARG 743": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D ARG 743": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13162 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Unusual residues: {'6EU': 1, '6O8': 1, '6O9': 1, '6OE': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'6O9': 1, '6OE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'6O9': 2, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.38, per 1000 atoms: 0.56 Number of scatterers: 13162 At special positions: 0 Unit cell: (120.344, 120.344, 110.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 16 15.00 O 2248 8.00 N 2098 7.00 C 8710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.4 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 4 sheets defined 54.2% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.591A pdb=" N SER A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.769A pdb=" N GLN A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 498 removed outlier: 3.559A pdb=" N PHE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 539 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 543 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 551 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 598 removed outlier: 4.288A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 585 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.530A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.581A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 696 No H-bonds generated for 'chain 'A' and resid 693 through 696' Processing helix chain 'A' and resid 698 through 712 removed outlier: 3.900A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 719 No H-bonds generated for 'chain 'A' and resid 716 through 719' Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.592A pdb=" N SER B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.768A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 539 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 553 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 598 removed outlier: 4.289A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 585 " --> pdb=" O MET B 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.530A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.580A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 696 No H-bonds generated for 'chain 'B' and resid 693 through 696' Processing helix chain 'B' and resid 698 through 712 removed outlier: 3.898A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 719 No H-bonds generated for 'chain 'B' and resid 716 through 719' Processing helix chain 'C' and resid 336 through 343 removed outlier: 3.593A pdb=" N SER C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.768A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 539 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 598 removed outlier: 4.288A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU C 585 " --> pdb=" O MET C 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.529A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.581A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 696 No H-bonds generated for 'chain 'C' and resid 693 through 696' Processing helix chain 'C' and resid 698 through 712 removed outlier: 3.899A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 719 No H-bonds generated for 'chain 'C' and resid 716 through 719' Processing helix chain 'D' and resid 336 through 343 removed outlier: 3.592A pdb=" N SER D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 419 through 428 removed outlier: 3.769A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 498 removed outlier: 3.560A pdb=" N PHE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.514A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 554 removed outlier: 3.730A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 539 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE D 543 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN D 551 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 553 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 removed outlier: 3.565A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 598 removed outlier: 4.287A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.529A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 4.080A pdb=" N LEU D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.580A pdb=" N ILE D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 696 No H-bonds generated for 'chain 'D' and resid 693 through 696' Processing helix chain 'D' and resid 698 through 712 removed outlier: 3.900A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 719 No H-bonds generated for 'chain 'D' and resid 716 through 719' Processing sheet with id= A, first strand: chain 'A' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 743 through 746 removed outlier: 6.099A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1632 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: 3.05 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1902 1.30 - 1.44: 4159 1.44 - 1.58: 7249 1.58 - 1.71: 32 1.71 - 1.85: 144 Bond restraints: 13486 Sorted by residual: bond pdb=" CAV 6EU D 805 " pdb=" CBB 6EU D 805 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" CAV 6EU C 803 " pdb=" CBB 6EU C 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU B 803 " pdb=" CBB 6EU B 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU A 804 " pdb=" CBB 6EU A 804 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAR 6EU B 803 " pdb=" CAZ 6EU B 803 " ideal model delta sigma weight residual 1.538 1.373 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 13481 not shown) Histogram of bond angle deviations from ideal: 95.48 - 105.62: 226 105.62 - 115.77: 8067 115.77 - 125.91: 9842 125.91 - 136.05: 201 136.05 - 146.19: 4 Bond angle restraints: 18340 Sorted by residual: angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta sigma weight residual 127.00 146.19 -19.19 2.40e+00 1.74e-01 6.40e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta sigma weight residual 127.00 146.15 -19.15 2.40e+00 1.74e-01 6.37e+01 angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 120.60 105.11 15.49 2.20e+00 2.07e-01 4.96e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CD PRO E 24 " ideal model delta sigma weight residual 120.60 105.15 15.45 2.20e+00 2.07e-01 4.93e+01 angle pdb=" O04 6O9 E 101 " pdb=" P05 6O9 E 101 " pdb=" O08 6O9 E 101 " ideal model delta sigma weight residual 93.00 108.99 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 18335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 7865 34.85 - 69.70: 134 69.70 - 104.54: 37 104.54 - 139.39: 29 139.39 - 174.24: 23 Dihedral angle restraints: 8088 sinusoidal: 3036 harmonic: 5052 Sorted by residual: dihedral pdb=" CA GLU A 416 " pdb=" C GLU A 416 " pdb=" N PRO A 417 " pdb=" CA PRO A 417 " ideal model delta harmonic sigma weight residual 180.00 133.67 46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA GLU C 416 " pdb=" C GLU C 416 " pdb=" N PRO C 417 " pdb=" CA PRO C 417 " ideal model delta harmonic sigma weight residual 180.00 133.70 46.30 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA GLU B 416 " pdb=" C GLU B 416 " pdb=" N PRO B 417 " pdb=" CA PRO B 417 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1639 0.079 - 0.157: 343 0.157 - 0.236: 38 0.236 - 0.314: 10 0.314 - 0.393: 8 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CAR 6EU A 804 " pdb=" CAO 6EU A 804 " pdb=" CAU 6EU A 804 " pdb=" CAZ 6EU A 804 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU C 803 " pdb=" CAO 6EU C 803 " pdb=" CAU 6EU C 803 " pdb=" CAZ 6EU C 803 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU D 805 " pdb=" CAO 6EU D 805 " pdb=" CAU 6EU D 805 " pdb=" CAZ 6EU D 805 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 2035 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 455 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 456 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 455 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO D 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 455 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO C 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 456 " -0.035 5.00e-02 4.00e+02 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 32 2.38 - 3.01: 6678 3.01 - 3.64: 19147 3.64 - 4.27: 29079 4.27 - 4.90: 47636 Nonbonded interactions: 102572 Sorted by model distance: nonbonded pdb=" O GLU F 26 " pdb=" O07 6OE F 103 " model vdw 1.744 3.040 nonbonded pdb=" O GLU E 26 " pdb=" O07 6OE E 102 " model vdw 1.819 3.040 nonbonded pdb=" OD1 ASN B 437 " pdb=" O06 6O8 B 801 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN A 437 " pdb=" O06 6O8 A 801 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN C 437 " pdb=" O06 6O8 C 801 " model vdw 2.162 3.040 ... (remaining 102567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 335 through 751 or resid 801)) selection = (chain 'B' and (resid 335 through 751 or resid 801)) selection = (chain 'C' and (resid 335 through 751 or resid 801)) selection = (chain 'D' and (resid 335 through 751 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 1 through 75 or resid 101)) selection = (chain 'F' and (resid 1 through 75 or resid 101)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.840 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 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:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.014 0.194 13486 Z= 0.942 Angle : 1.437 19.195 18340 Z= 0.660 Chirality : 0.067 0.393 2038 Planarity : 0.006 0.063 2224 Dihedral : 19.899 174.240 4824 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.68 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.45 (0.12), residues: 1714 helix: -4.13 (0.08), residues: 988 sheet: -4.38 (0.62), residues: 52 loop : -4.31 (0.17), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 53 HIS 0.004 0.001 HIS C 358 PHE 0.034 0.003 PHE D 448 TYR 0.022 0.003 TYR C 653 ARG 0.010 0.002 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7579 (mmm) cc_final: 0.7331 (mmp) REVERT: A 639 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8383 (mtpt) REVERT: B 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8343 (mtpt) REVERT: C 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8254 (mtpt) REVERT: D 445 MET cc_start: 0.7699 (mmm) cc_final: 0.7418 (mmp) REVERT: D 639 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8239 (mtpt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 1.3575 time to fit residues: 420.9760 Evaluate side-chains 189 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 628 ASN A 691 GLN B 628 ASN B 691 GLN C 628 ASN C 691 GLN D 437 ASN D 494 GLN D 628 ASN D 691 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13486 Z= 0.177 Angle : 0.606 8.271 18340 Z= 0.305 Chirality : 0.039 0.183 2038 Planarity : 0.005 0.063 2224 Dihedral : 19.486 179.736 2612 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.17 % Allowed : 14.49 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -4.10 (0.16), residues: 1714 helix: -1.83 (0.13), residues: 1008 sheet: -4.53 (0.50), residues: 64 loop : -3.92 (0.19), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 749 HIS 0.001 0.000 HIS B 410 PHE 0.013 0.001 PHE D 448 TYR 0.016 0.001 TYR E 22 ARG 0.003 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 252 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 697 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.7113 (t60) REVERT: C 697 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.7054 (t60) REVERT: D 568 MET cc_start: 0.7955 (ptp) cc_final: 0.7562 (ptp) REVERT: D 697 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7133 (t60) outliers start: 33 outliers final: 12 residues processed: 262 average time/residue: 0.9446 time to fit residues: 275.2504 Evaluate side-chains 218 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 697 TRP Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 30.0000 chunk 52 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 628 ASN B 437 ASN B 494 GLN B 628 ASN C 354 GLN C 437 ASN C 628 ASN D 494 GLN D 628 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13486 Z= 0.151 Angle : 0.569 7.753 18340 Z= 0.280 Chirality : 0.039 0.176 2038 Planarity : 0.004 0.052 2224 Dihedral : 16.882 167.409 2612 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.17 % Allowed : 16.99 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.19), residues: 1714 helix: -0.42 (0.16), residues: 1008 sheet: -4.29 (0.51), residues: 64 loop : -3.66 (0.20), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 740 HIS 0.004 0.001 HIS A 358 PHE 0.010 0.001 PHE C 448 TYR 0.013 0.001 TYR D 653 ARG 0.002 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 1.299 Fit side-chains REVERT: A 418 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7766 (pp) REVERT: D 418 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7822 (pp) outliers start: 33 outliers final: 7 residues processed: 247 average time/residue: 1.0372 time to fit residues: 283.2021 Evaluate side-chains 215 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.6980 chunk 116 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 628 ASN B 494 GLN B 628 ASN C 354 GLN C 628 ASN D 494 GLN D 628 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13486 Z= 0.143 Angle : 0.535 7.149 18340 Z= 0.268 Chirality : 0.039 0.167 2038 Planarity : 0.003 0.054 2224 Dihedral : 15.494 151.632 2612 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.26 % Allowed : 20.92 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.20), residues: 1714 helix: 0.39 (0.17), residues: 988 sheet: -4.19 (0.50), residues: 64 loop : -3.59 (0.19), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 740 HIS 0.001 0.000 HIS C 358 PHE 0.009 0.001 PHE C 448 TYR 0.015 0.001 TYR E 22 ARG 0.002 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: D 418 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7697 (pp) outliers start: 34 outliers final: 5 residues processed: 256 average time/residue: 1.0081 time to fit residues: 288.3978 Evaluate side-chains 231 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 418 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN B 494 GLN B 628 ASN C 354 GLN C 494 GLN C 628 ASN D 354 GLN D 494 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13486 Z= 0.216 Angle : 0.558 7.532 18340 Z= 0.278 Chirality : 0.040 0.168 2038 Planarity : 0.003 0.050 2224 Dihedral : 14.807 125.269 2612 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.65 % Allowed : 22.74 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.20), residues: 1714 helix: 0.59 (0.17), residues: 1016 sheet: -4.14 (0.48), residues: 64 loop : -3.69 (0.20), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 740 HIS 0.001 0.000 HIS B 358 PHE 0.011 0.001 PHE B 448 TYR 0.013 0.001 TYR F 22 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 524 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7265 (mp) REVERT: D 524 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7302 (mp) outliers start: 38 outliers final: 9 residues processed: 237 average time/residue: 1.0943 time to fit residues: 287.8058 Evaluate side-chains 222 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 211 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN B 628 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN C 494 GLN C 628 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 494 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13486 Z= 0.226 Angle : 0.561 7.014 18340 Z= 0.280 Chirality : 0.041 0.220 2038 Planarity : 0.003 0.052 2224 Dihedral : 14.119 116.203 2612 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.13 % Allowed : 22.94 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1714 helix: 0.71 (0.17), residues: 1024 sheet: -4.10 (0.49), residues: 64 loop : -3.60 (0.20), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 740 HIS 0.002 0.000 HIS C 358 PHE 0.011 0.001 PHE B 448 TYR 0.014 0.001 TYR E 22 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 1.613 Fit side-chains REVERT: D 644 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7390 (ptp) REVERT: D 697 TRP cc_start: 0.7276 (OUTLIER) cc_final: 0.7010 (t60) outliers start: 43 outliers final: 14 residues processed: 231 average time/residue: 1.0267 time to fit residues: 262.2212 Evaluate side-chains 224 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN C 494 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 494 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 13486 Z= 0.148 Angle : 0.557 10.468 18340 Z= 0.279 Chirality : 0.040 0.344 2038 Planarity : 0.003 0.049 2224 Dihedral : 13.581 114.578 2612 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.42 % Rotamer: Outliers : 3.07 % Allowed : 24.47 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1714 helix: 1.14 (0.17), residues: 1000 sheet: -4.04 (0.50), residues: 64 loop : -3.48 (0.20), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 11 HIS 0.007 0.001 HIS F 30 PHE 0.007 0.001 PHE D 489 TYR 0.023 0.001 TYR F 22 ARG 0.001 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.416 Fit side-chains REVERT: A 396 LEU cc_start: 0.8036 (mt) cc_final: 0.7815 (mt) REVERT: A 677 MET cc_start: 0.8240 (ttm) cc_final: 0.7767 (mtp) REVERT: B 396 LEU cc_start: 0.8061 (mt) cc_final: 0.7861 (mt) outliers start: 32 outliers final: 8 residues processed: 253 average time/residue: 0.9709 time to fit residues: 273.2368 Evaluate side-chains 234 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.0980 chunk 97 optimal weight: 0.0030 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN B 354 GLN B 494 GLN B 628 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN C 628 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13486 Z= 0.138 Angle : 0.549 8.775 18340 Z= 0.274 Chirality : 0.040 0.329 2038 Planarity : 0.003 0.058 2224 Dihedral : 13.096 112.613 2612 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.92 % Allowed : 27.06 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.21), residues: 1714 helix: 1.23 (0.17), residues: 1024 sheet: -3.73 (0.47), residues: 84 loop : -3.63 (0.21), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 11 HIS 0.003 0.000 HIS E 30 PHE 0.006 0.001 PHE C 489 TYR 0.020 0.001 TYR F 22 ARG 0.001 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.559 Fit side-chains REVERT: A 396 LEU cc_start: 0.8032 (mt) cc_final: 0.7810 (mt) REVERT: A 677 MET cc_start: 0.8186 (ttm) cc_final: 0.7728 (mtp) REVERT: B 396 LEU cc_start: 0.7974 (mt) cc_final: 0.7745 (mt) REVERT: D 396 LEU cc_start: 0.7996 (mt) cc_final: 0.7745 (mt) outliers start: 20 outliers final: 4 residues processed: 245 average time/residue: 0.9859 time to fit residues: 268.9042 Evaluate side-chains 235 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 635 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.0870 chunk 143 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN B 354 GLN B 628 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13486 Z= 0.179 Angle : 0.587 8.827 18340 Z= 0.291 Chirality : 0.041 0.306 2038 Planarity : 0.003 0.048 2224 Dihedral : 12.854 107.288 2612 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.40 % Allowed : 27.54 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.87 (0.21), residues: 1714 helix: 1.29 (0.17), residues: 1024 sheet: -3.61 (0.48), residues: 84 loop : -3.60 (0.21), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 11 HIS 0.001 0.000 HIS D 358 PHE 0.010 0.001 PHE B 582 TYR 0.021 0.001 TYR F 22 ARG 0.002 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.556 Fit side-chains REVERT: A 585 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8518 (mp) REVERT: A 677 MET cc_start: 0.8209 (ttm) cc_final: 0.7608 (mtp) REVERT: C 523 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6933 (ttp) REVERT: C 585 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8523 (mp) REVERT: C 677 MET cc_start: 0.8146 (ttm) cc_final: 0.7781 (mtp) REVERT: D 585 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8398 (mp) outliers start: 25 outliers final: 9 residues processed: 229 average time/residue: 1.0351 time to fit residues: 262.2221 Evaluate side-chains 230 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13486 Z= 0.173 Angle : 0.590 10.256 18340 Z= 0.290 Chirality : 0.041 0.295 2038 Planarity : 0.003 0.049 2224 Dihedral : 12.647 104.823 2612 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.92 % Allowed : 28.21 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1714 helix: 1.37 (0.16), residues: 1028 sheet: -3.54 (0.49), residues: 84 loop : -3.43 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 11 HIS 0.001 0.000 HIS E 30 PHE 0.009 0.001 PHE B 582 TYR 0.022 0.001 TYR F 22 ARG 0.001 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 1.380 Fit side-chains REVERT: A 412 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6320 (mmt) REVERT: B 412 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6235 (mmt) REVERT: B 585 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8520 (mp) REVERT: C 523 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6848 (ttp) REVERT: C 677 MET cc_start: 0.8140 (ttm) cc_final: 0.7807 (mtp) REVERT: D 523 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6803 (ttp) outliers start: 20 outliers final: 7 residues processed: 228 average time/residue: 1.0544 time to fit residues: 265.5653 Evaluate side-chains 226 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 19 optimal weight: 0.0040 chunk 37 optimal weight: 50.0000 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN B 628 ASN C 628 ASN ** C 676 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 = 0.3794 r_free = 0.3794 target = 0.134749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099096 restraints weight = 21395.709| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.60 r_work: 0.3108 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13486 Z= 0.168 Angle : 0.584 9.068 18340 Z= 0.288 Chirality : 0.040 0.290 2038 Planarity : 0.003 0.050 2224 Dihedral : 12.158 95.086 2612 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.02 % Allowed : 28.50 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1714 helix: 1.50 (0.16), residues: 1020 sheet: -3.49 (0.49), residues: 84 loop : -3.21 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 11 HIS 0.002 0.000 HIS B 358 PHE 0.011 0.001 PHE C 582 TYR 0.021 0.001 TYR F 22 ARG 0.001 0.000 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.74 seconds wall clock time: 85 minutes 5.42 seconds (5105.42 seconds total)