Starting phenix.real_space_refine on Sat Mar 16 09:15:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6opn_20150/03_2024/6opn_20150_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 8949 2.51 5 N 2418 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 634": "OE1" <-> "OE2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 466": "OE1" <-> "OE2" Residue "G TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 634": "OE1" <-> "OE2" Residue "H TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 14241 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2753 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 6 Chain: "B" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "D" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2753 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 6 Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "G" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2753 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 6 Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 760 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'N07': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'N07': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'N07': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.56, per 1000 atoms: 0.53 Number of scatterers: 14241 At special positions: 0 Unit cell: (147.29, 150.38, 111.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2784 8.00 N 2418 7.00 C 8949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.21 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.05 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.02 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.21 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.21 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 332 " " NAG A 612 " - " ASN A 362 " " NAG A 613 " - " ASN A 386 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 413 " " NAG A 616 " - " ASN A 448 " " NAG D 601 " - " ASN D 234 " " NAG D 609 " - " ASN D 276 " " NAG D 610 " - " ASN D 295 " " NAG D 611 " - " ASN D 332 " " NAG D 612 " - " ASN D 362 " " NAG D 613 " - " ASN D 386 " " NAG D 614 " - " ASN D 392 " " NAG D 615 " - " ASN D 413 " " NAG D 616 " - " ASN D 448 " " NAG G 601 " - " ASN G 234 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 295 " " NAG G 611 " - " ASN G 332 " " NAG G 612 " - " ASN G 362 " " NAG G 613 " - " ASN G 386 " " NAG G 614 " - " ASN G 392 " " NAG G 615 " - " ASN G 413 " " NAG G 616 " - " ASN G 448 " " NAG J 1 " - " ASN A 241 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN D 241 " " NAG M 1 " - " ASN D 262 " " NAG N 1 " - " ASN G 241 " " NAG O 1 " - " ASN G 262 " Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 24 sheets defined 27.3% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.891A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.372A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.965A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.979A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 546 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.650A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.931A pdb=" N THR B 639 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.024A pdb=" N ASP C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'D' and resid 65 through 73 removed outlier: 3.891A pdb=" N HIS D 72 " --> pdb=" O VAL D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 100 through 115 removed outlier: 4.372A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 351 removed outlier: 3.965A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 475 through 485 removed outlier: 3.978A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 546 Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.650A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY E 594 " --> pdb=" O GLN E 590 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE E 595 " --> pdb=" O GLN E 591 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 614 No H-bonds generated for 'chain 'E' and resid 612 through 614' Processing helix chain 'E' and resid 619 through 625 Processing helix chain 'E' and resid 628 through 634 Processing helix chain 'E' and resid 636 through 658 removed outlier: 3.931A pdb=" N THR E 639 " --> pdb=" O ASP E 636 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN E 640 " --> pdb=" O ASN E 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 64 removed outlier: 4.024A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'G' and resid 65 through 73 removed outlier: 3.892A pdb=" N HIS G 72 " --> pdb=" O VAL G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 100 through 115 removed outlier: 4.372A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 removed outlier: 3.964A pdb=" N GLU G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 372 No H-bonds generated for 'chain 'G' and resid 369 through 372' Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 475 through 485 removed outlier: 3.979A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS G 485 " --> pdb=" O SER G 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 546 Processing helix chain 'H' and resid 570 through 596 removed outlier: 3.650A pdb=" N ARG H 579 " --> pdb=" O GLN H 575 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY H 594 " --> pdb=" O GLN H 590 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE H 595 " --> pdb=" O GLN H 591 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP H 596 " --> pdb=" O LEU H 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 612 through 614 No H-bonds generated for 'chain 'H' and resid 612 through 614' Processing helix chain 'H' and resid 619 through 625 Processing helix chain 'H' and resid 628 through 634 Processing helix chain 'H' and resid 636 through 658 removed outlier: 3.931A pdb=" N THR H 639 " --> pdb=" O ASP H 636 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLN H 640 " --> pdb=" O ASN H 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 4.024A pdb=" N ASP I 63 " --> pdb=" O SER I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 78 No H-bonds generated for 'chain 'I' and resid 76 through 78' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= E, first strand: chain 'A' and resid 271 through 273 Processing sheet with id= F, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.283A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= H, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.670A pdb=" N GLU C 91 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= J, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= K, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= M, first strand: chain 'D' and resid 271 through 273 Processing sheet with id= N, first strand: chain 'D' and resid 374 through 378 removed outlier: 4.283A pdb=" N SER D 334 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N GLU D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 12 through 17 Processing sheet with id= P, first strand: chain 'F' and resid 91 through 95 removed outlier: 3.671A pdb=" N GLU F 91 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN F 30 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS F 35 " --> pdb=" O ASN F 30 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 35 through 40 Processing sheet with id= R, first strand: chain 'G' and resid 45 through 47 Processing sheet with id= S, first strand: chain 'G' and resid 53 through 56 Processing sheet with id= T, first strand: chain 'G' and resid 199 through 202 Processing sheet with id= U, first strand: chain 'G' and resid 271 through 273 Processing sheet with id= V, first strand: chain 'G' and resid 374 through 378 removed outlier: 4.283A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 12 through 17 Processing sheet with id= X, first strand: chain 'I' and resid 91 through 95 removed outlier: 3.671A pdb=" N GLU I 91 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS I 35 " --> pdb=" O ASN I 30 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1332 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: 4.34 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3296 1.32 - 1.45: 3933 1.45 - 1.58: 7125 1.58 - 1.71: 31 1.71 - 1.84: 117 Bond restraints: 14502 Sorted by residual: bond pdb=" C1 NAG D 601 " pdb=" O5 NAG D 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG G 601 " pdb=" O5 NAG G 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.88e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 NAG A 615 " pdb=" O5 NAG A 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG D 615 " pdb=" O5 NAG D 615 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 14497 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.18: 235 104.18 - 111.82: 6863 111.82 - 119.46: 5813 119.46 - 127.10: 6523 127.10 - 134.74: 213 Bond angle restraints: 19647 Sorted by residual: angle pdb=" C PRO A 437 " pdb=" N PRO A 438 " pdb=" CA PRO A 438 " ideal model delta sigma weight residual 120.03 128.18 -8.15 9.90e-01 1.02e+00 6.78e+01 angle pdb=" C PRO G 437 " pdb=" N PRO G 438 " pdb=" CA PRO G 438 " ideal model delta sigma weight residual 120.03 128.17 -8.14 9.90e-01 1.02e+00 6.75e+01 angle pdb=" C PRO D 437 " pdb=" N PRO D 438 " pdb=" CA PRO D 438 " ideal model delta sigma weight residual 120.03 128.15 -8.12 9.90e-01 1.02e+00 6.73e+01 angle pdb=" C ALA G 436 " pdb=" N PRO G 437 " pdb=" CA PRO G 437 " ideal model delta sigma weight residual 120.38 128.28 -7.90 1.03e+00 9.43e-01 5.88e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 120.38 128.26 -7.88 1.03e+00 9.43e-01 5.85e+01 ... (remaining 19642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 9024 22.20 - 44.39: 252 44.39 - 66.59: 66 66.59 - 88.78: 30 88.78 - 110.98: 12 Dihedral angle restraints: 9384 sinusoidal: 4464 harmonic: 4920 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.87 85.87 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS D 119 " pdb=" SG CYS D 119 " pdb=" SG CYS D 205 " pdb=" CB CYS D 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.86 85.86 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -171.85 85.85 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 9381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1732 0.110 - 0.220: 554 0.220 - 0.330: 60 0.330 - 0.440: 9 0.440 - 0.550: 3 Chirality restraints: 2358 Sorted by residual: chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.60e+01 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.59e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.52e+01 ... (remaining 2355 not shown) Planarity restraints: 2460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 332 " -0.060 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" CG ASN G 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN G 332 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN G 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG G 611 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.062 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN D 392 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG D 614 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " -0.060 2.00e-02 2.50e+03 6.49e-02 5.27e+01 pdb=" CG ASN A 332 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG A 611 " -0.079 2.00e-02 2.50e+03 ... (remaining 2457 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4097 2.81 - 3.34: 13026 3.34 - 3.86: 23768 3.86 - 4.38: 27977 4.38 - 4.90: 45137 Nonbonded interactions: 114005 Sorted by model distance: nonbonded pdb=" OG1 THR D 373 " pdb=" O CYS D 385 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR G 373 " pdb=" O CYS G 385 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR A 373 " pdb=" O CYS A 385 " model vdw 2.295 2.440 nonbonded pdb=" O4 NAG D 614 " pdb=" O6 NAG D 614 " model vdw 2.391 2.440 nonbonded pdb=" O4 NAG G 614 " pdb=" O6 NAG G 614 " model vdw 2.391 2.440 ... (remaining 114000 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } 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 group one per residue 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: 1.300 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: 5.800 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.430 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.022 0.169 14502 Z= 1.393 Angle : 1.781 15.840 19647 Z= 1.152 Chirality : 0.103 0.550 2358 Planarity : 0.009 0.057 2427 Dihedral : 12.345 110.976 6090 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1653 helix: 0.40 (0.22), residues: 405 sheet: 1.27 (0.24), residues: 381 loop : 0.08 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.010 TRP C 28 HIS 0.007 0.002 HIS A 330 PHE 0.029 0.007 PHE A 353 TYR 0.028 0.006 TYR D 484 ARG 0.007 0.001 ARG D 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7717 (ttm) cc_final: 0.7513 (ttm) REVERT: B 530 MET cc_start: 0.7404 (mtm) cc_final: 0.6759 (mtp) REVERT: D 371 ILE cc_start: 0.8266 (pt) cc_final: 0.7815 (pt) REVERT: E 530 MET cc_start: 0.7434 (mtm) cc_final: 0.6814 (mtp) REVERT: F 1 LYS cc_start: 0.7755 (pttm) cc_final: 0.7500 (pttp) REVERT: G 371 ILE cc_start: 0.8274 (pt) cc_final: 0.7771 (pt) REVERT: H 530 MET cc_start: 0.7459 (mtm) cc_final: 0.6892 (mtp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2962 time to fit residues: 170.9955 Evaluate side-chains 183 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 5.9990 chunk 127 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 25 GLN C 40 GLN E 652 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 40 GLN H 652 GLN I 20 GLN I 25 GLN I 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14502 Z= 0.216 Angle : 0.798 10.727 19647 Z= 0.416 Chirality : 0.049 0.168 2358 Planarity : 0.005 0.049 2427 Dihedral : 9.336 66.618 2805 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.17 % Allowed : 9.70 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1653 helix: 0.60 (0.24), residues: 423 sheet: 0.63 (0.25), residues: 303 loop : -0.29 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 96 HIS 0.008 0.002 HIS E 641 PHE 0.020 0.003 PHE G 233 TYR 0.017 0.002 TYR D 486 ARG 0.007 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.6354 (t80) cc_final: 0.6090 (t80) REVERT: A 475 MET cc_start: 0.6519 (mmp) cc_final: 0.6313 (mmm) REVERT: A 482 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5999 (mm-30) REVERT: B 530 MET cc_start: 0.7384 (mtm) cc_final: 0.7125 (mtp) REVERT: B 615 SER cc_start: 0.8541 (p) cc_final: 0.8339 (t) REVERT: C 69 LEU cc_start: 0.8001 (mp) cc_final: 0.7253 (mp) REVERT: D 482 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6335 (mm-30) REVERT: E 530 MET cc_start: 0.7446 (mtm) cc_final: 0.7129 (mtp) REVERT: E 656 ASN cc_start: 0.8789 (m-40) cc_final: 0.8253 (m-40) REVERT: F 69 LEU cc_start: 0.7673 (mp) cc_final: 0.7109 (mp) REVERT: G 40 TYR cc_start: 0.6305 (t80) cc_final: 0.5899 (t80) REVERT: G 482 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6145 (mm-30) REVERT: H 530 MET cc_start: 0.7517 (mtm) cc_final: 0.7122 (mtp) REVERT: H 656 ASN cc_start: 0.8828 (m-40) cc_final: 0.8330 (m-40) REVERT: I 1 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6860 (pptt) REVERT: I 25 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7463 (pp30) REVERT: I 69 LEU cc_start: 0.7910 (mp) cc_final: 0.7221 (mp) outliers start: 48 outliers final: 25 residues processed: 278 average time/residue: 0.2712 time to fit residues: 108.0952 Evaluate side-chains 201 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 1 LYS Chi-restraints excluded: chain I residue 25 GLN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14502 Z= 0.282 Angle : 0.744 10.632 19647 Z= 0.382 Chirality : 0.046 0.150 2358 Planarity : 0.005 0.048 2427 Dihedral : 8.366 59.707 2805 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.10 % Allowed : 12.74 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 1653 helix: 0.58 (0.25), residues: 408 sheet: 0.04 (0.26), residues: 324 loop : -0.27 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 28 HIS 0.007 0.002 HIS C 27 PHE 0.022 0.003 PHE B 522 TYR 0.014 0.002 TYR A 484 ARG 0.005 0.001 ARG G 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.6281 (t80) cc_final: 0.5870 (t80) REVERT: A 482 GLU cc_start: 0.6719 (mm-30) cc_final: 0.6308 (mm-30) REVERT: B 530 MET cc_start: 0.7622 (mtm) cc_final: 0.7344 (mtp) REVERT: C 63 ASP cc_start: 0.8403 (t0) cc_final: 0.8128 (p0) REVERT: C 92 GLU cc_start: 0.7783 (mp0) cc_final: 0.7527 (pm20) REVERT: D 217 TYR cc_start: 0.6137 (m-80) cc_final: 0.5795 (m-80) REVERT: D 482 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6442 (mm-30) REVERT: F 63 ASP cc_start: 0.8687 (t0) cc_final: 0.8444 (p0) REVERT: F 69 LEU cc_start: 0.7169 (mp) cc_final: 0.6957 (tp) REVERT: G 217 TYR cc_start: 0.6278 (m-80) cc_final: 0.5879 (m-80) REVERT: G 482 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6293 (mm-30) REVERT: H 530 MET cc_start: 0.7741 (mtm) cc_final: 0.7503 (mtp) REVERT: I 69 LEU cc_start: 0.7295 (mp) cc_final: 0.7013 (tp) REVERT: I 73 ASN cc_start: 0.8838 (t0) cc_final: 0.8558 (t0) outliers start: 47 outliers final: 33 residues processed: 228 average time/residue: 0.2599 time to fit residues: 86.7297 Evaluate side-chains 191 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 349 LEU Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 203 GLN ** H 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14502 Z= 0.188 Angle : 0.667 8.342 19647 Z= 0.339 Chirality : 0.044 0.154 2358 Planarity : 0.005 0.052 2427 Dihedral : 7.228 58.461 2805 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.63 % Allowed : 13.14 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1653 helix: 0.79 (0.26), residues: 405 sheet: 0.14 (0.25), residues: 354 loop : -0.33 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 28 HIS 0.003 0.001 HIS H 641 PHE 0.010 0.002 PHE G 383 TYR 0.013 0.002 TYR A 484 ARG 0.006 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.6300 (t80) cc_final: 0.5947 (t80) REVERT: A 449 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7165 (pt) REVERT: A 482 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6335 (mm-30) REVERT: B 530 MET cc_start: 0.7572 (mtm) cc_final: 0.7281 (mtp) REVERT: B 626 MET cc_start: 0.6915 (mtp) cc_final: 0.6629 (mtp) REVERT: B 656 ASN cc_start: 0.8857 (m-40) cc_final: 0.8529 (m-40) REVERT: D 217 TYR cc_start: 0.5791 (m-80) cc_final: 0.5516 (m-80) REVERT: D 449 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7132 (pt) REVERT: D 482 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6240 (mm-30) REVERT: F 63 ASP cc_start: 0.8765 (t0) cc_final: 0.8502 (p0) REVERT: G 257 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7874 (m) REVERT: G 449 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7503 (pt) REVERT: G 482 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6271 (mm-30) REVERT: H 530 MET cc_start: 0.7684 (mtm) cc_final: 0.6643 (mtm) REVERT: H 626 MET cc_start: 0.6998 (ttm) cc_final: 0.6120 (mtp) REVERT: I 69 LEU cc_start: 0.7141 (mp) cc_final: 0.6886 (tp) outliers start: 55 outliers final: 28 residues processed: 224 average time/residue: 0.2420 time to fit residues: 81.6372 Evaluate side-chains 192 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS H 656 ASN I 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14502 Z= 0.209 Angle : 0.668 8.136 19647 Z= 0.340 Chirality : 0.044 0.143 2358 Planarity : 0.005 0.046 2427 Dihedral : 6.669 53.446 2805 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.56 % Allowed : 13.33 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1653 helix: 0.78 (0.26), residues: 402 sheet: 0.35 (0.27), residues: 330 loop : -0.49 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 28 HIS 0.005 0.001 HIS I 27 PHE 0.012 0.002 PHE H 522 TYR 0.012 0.002 TYR G 40 ARG 0.005 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 1.585 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 45 TRP cc_start: 0.6784 (OUTLIER) cc_final: 0.6034 (m-90) REVERT: A 449 ILE cc_start: 0.7601 (OUTLIER) cc_final: 0.7207 (pt) REVERT: A 482 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6437 (mm-30) REVERT: B 530 MET cc_start: 0.7641 (mtm) cc_final: 0.7358 (mtp) REVERT: B 626 MET cc_start: 0.7029 (mtp) cc_final: 0.6805 (mtp) REVERT: C 28 TRP cc_start: 0.7593 (t-100) cc_final: 0.7020 (m-90) REVERT: C 73 ASN cc_start: 0.8944 (t0) cc_final: 0.8713 (t0) REVERT: D 104 MET cc_start: 0.8478 (tpt) cc_final: 0.7818 (tpt) REVERT: D 217 TYR cc_start: 0.5678 (m-80) cc_final: 0.5469 (m-80) REVERT: D 449 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7208 (pt) REVERT: D 482 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6347 (mm-30) REVERT: E 530 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7522 (mtp) REVERT: F 63 ASP cc_start: 0.8830 (t0) cc_final: 0.8533 (p0) REVERT: F 64 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7957 (mp10) REVERT: G 449 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7485 (pt) REVERT: G 482 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6446 (mm-30) REVERT: H 530 MET cc_start: 0.7561 (mtm) cc_final: 0.6769 (mtm) outliers start: 54 outliers final: 35 residues processed: 221 average time/residue: 0.2517 time to fit residues: 82.2265 Evaluate side-chains 205 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 530 MET Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 162 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14502 Z= 0.172 Angle : 0.638 7.998 19647 Z= 0.321 Chirality : 0.043 0.139 2358 Planarity : 0.004 0.047 2427 Dihedral : 6.192 50.515 2805 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.64 % Allowed : 14.98 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1653 helix: 0.81 (0.26), residues: 402 sheet: 0.27 (0.26), residues: 366 loop : -0.56 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 28 HIS 0.003 0.001 HIS G 216 PHE 0.009 0.001 PHE A 383 TYR 0.015 0.001 TYR G 40 ARG 0.006 0.000 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.6689 (OUTLIER) cc_final: 0.5974 (m-90) REVERT: A 449 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7264 (pt) REVERT: A 482 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6522 (mm-30) REVERT: D 104 MET cc_start: 0.8402 (tpt) cc_final: 0.7799 (tpt) REVERT: D 449 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7158 (pt) REVERT: D 482 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6362 (mm-30) REVERT: E 626 MET cc_start: 0.6813 (ttm) cc_final: 0.6436 (mtp) REVERT: F 63 ASP cc_start: 0.8853 (t0) cc_final: 0.8613 (p0) REVERT: F 64 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8000 (mp10) REVERT: G 449 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7504 (pt) REVERT: G 482 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6446 (mm-30) REVERT: H 530 MET cc_start: 0.7532 (mtm) cc_final: 0.7044 (mtm) outliers start: 40 outliers final: 27 residues processed: 205 average time/residue: 0.2376 time to fit residues: 74.2550 Evaluate side-chains 196 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 96 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 0.0040 chunk 74 optimal weight: 10.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 66 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14502 Z= 0.173 Angle : 0.634 8.005 19647 Z= 0.320 Chirality : 0.043 0.170 2358 Planarity : 0.004 0.046 2427 Dihedral : 5.904 46.823 2805 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.51 % Allowed : 15.05 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1653 helix: 0.83 (0.26), residues: 402 sheet: 0.44 (0.27), residues: 342 loop : -0.62 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP C 28 HIS 0.003 0.001 HIS C 27 PHE 0.009 0.001 PHE B 522 TYR 0.025 0.001 TYR H 638 ARG 0.008 0.000 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 1.613 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: A 45 TRP cc_start: 0.6747 (OUTLIER) cc_final: 0.6051 (m-90) REVERT: A 449 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7286 (pt) REVERT: A 482 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 626 MET cc_start: 0.7006 (mtp) cc_final: 0.6787 (mtp) REVERT: D 449 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7118 (pt) REVERT: D 482 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6418 (mm-30) REVERT: F 64 GLN cc_start: 0.8426 (mm-40) cc_final: 0.8021 (mp10) REVERT: G 45 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.5806 (m-10) REVERT: G 449 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7502 (pt) REVERT: G 482 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6561 (mm-30) REVERT: H 530 MET cc_start: 0.7501 (mtm) cc_final: 0.6885 (mtm) REVERT: H 626 MET cc_start: 0.7060 (ttt) cc_final: 0.6618 (mtp) outliers start: 38 outliers final: 26 residues processed: 206 average time/residue: 0.2373 time to fit residues: 73.9258 Evaluate side-chains 196 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 96 TRP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14502 Z= 0.251 Angle : 0.697 9.727 19647 Z= 0.351 Chirality : 0.044 0.258 2358 Planarity : 0.005 0.045 2427 Dihedral : 6.122 42.344 2805 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.77 % Allowed : 15.91 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1653 helix: 0.62 (0.25), residues: 408 sheet: 0.13 (0.28), residues: 342 loop : -0.68 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 28 HIS 0.007 0.001 HIS I 27 PHE 0.017 0.002 PHE B 522 TYR 0.012 0.002 TYR G 40 ARG 0.007 0.001 ARG H 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.653 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: A 45 TRP cc_start: 0.6909 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: A 449 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7341 (pt) REVERT: D 104 MET cc_start: 0.8417 (tpt) cc_final: 0.7845 (tpt) REVERT: D 482 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6720 (mm-30) REVERT: G 45 TRP cc_start: 0.6899 (OUTLIER) cc_final: 0.5821 (m-10) REVERT: G 449 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7420 (pt) REVERT: G 482 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6689 (mm-30) REVERT: H 530 MET cc_start: 0.7747 (mtm) cc_final: 0.7073 (mtm) REVERT: H 626 MET cc_start: 0.7429 (ttt) cc_final: 0.7073 (mtp) outliers start: 42 outliers final: 33 residues processed: 203 average time/residue: 0.2380 time to fit residues: 73.0338 Evaluate side-chains 198 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 150 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14502 Z= 0.185 Angle : 0.652 8.290 19647 Z= 0.330 Chirality : 0.043 0.208 2358 Planarity : 0.004 0.044 2427 Dihedral : 5.802 40.343 2805 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.90 % Allowed : 16.11 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1653 helix: 0.73 (0.26), residues: 408 sheet: 0.15 (0.28), residues: 342 loop : -0.64 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 28 HIS 0.004 0.001 HIS G 216 PHE 0.010 0.001 PHE D 391 TYR 0.011 0.001 TYR A 486 ARG 0.011 0.001 ARG C 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 1.657 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: A 45 TRP cc_start: 0.6759 (OUTLIER) cc_final: 0.6097 (m-10) REVERT: A 449 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7307 (pt) REVERT: A 482 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6814 (mm-30) REVERT: C 54 ARG cc_start: 0.7002 (mpp80) cc_final: 0.6796 (mpp80) REVERT: C 63 ASP cc_start: 0.7815 (p0) cc_final: 0.7220 (p0) REVERT: C 64 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7925 (mm-40) REVERT: D 104 MET cc_start: 0.8345 (tpt) cc_final: 0.7777 (tpt) REVERT: D 482 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6729 (mm-30) REVERT: E 530 MET cc_start: 0.8221 (mtm) cc_final: 0.7823 (mtm) REVERT: G 45 TRP cc_start: 0.6753 (OUTLIER) cc_final: 0.5815 (m-10) REVERT: G 449 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7366 (pt) REVERT: G 482 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6720 (mm-30) REVERT: H 530 MET cc_start: 0.7711 (mtm) cc_final: 0.7015 (mtm) REVERT: H 626 MET cc_start: 0.7437 (ttt) cc_final: 0.7055 (mtp) outliers start: 44 outliers final: 36 residues processed: 209 average time/residue: 0.2488 time to fit residues: 78.4632 Evaluate side-chains 206 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 45 TRP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 45 TRP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.0570 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 167 optimal weight: 0.2980 chunk 154 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14502 Z= 0.180 Angle : 0.657 9.642 19647 Z= 0.328 Chirality : 0.043 0.196 2358 Planarity : 0.004 0.042 2427 Dihedral : 5.522 37.625 2805 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.31 % Allowed : 17.10 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1653 helix: 0.86 (0.26), residues: 408 sheet: 0.20 (0.28), residues: 342 loop : -0.58 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 28 HIS 0.003 0.001 HIS F 27 PHE 0.010 0.001 PHE A 210 TYR 0.011 0.001 TYR A 486 ARG 0.010 0.000 ARG I 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.730 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: A 45 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.6061 (m-10) REVERT: A 449 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7294 (pt) REVERT: A 482 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6775 (mm-30) REVERT: B 530 MET cc_start: 0.7764 (mmm) cc_final: 0.7310 (mmt) REVERT: B 633 LYS cc_start: 0.8218 (pptt) cc_final: 0.8009 (mptt) REVERT: C 54 ARG cc_start: 0.6893 (mpp80) cc_final: 0.6673 (mpp80) REVERT: D 104 MET cc_start: 0.8355 (tpt) cc_final: 0.7803 (tpt) REVERT: D 427 TRP cc_start: 0.8536 (p-90) cc_final: 0.8241 (p-90) REVERT: D 449 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7110 (pt) REVERT: D 482 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6721 (mm-30) REVERT: E 633 LYS cc_start: 0.8190 (pptt) cc_final: 0.7946 (mptt) REVERT: G 449 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7395 (pt) REVERT: G 482 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6681 (mm-30) REVERT: H 530 MET cc_start: 0.7673 (mtm) cc_final: 0.7060 (mtm) outliers start: 35 outliers final: 29 residues processed: 207 average time/residue: 0.2339 time to fit residues: 73.5469 Evaluate side-chains 206 residues out of total 1515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 449 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 629 MET Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 251 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 449 ILE Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain I residue 53 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.118411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.101469 restraints weight = 44018.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.104867 restraints weight = 23083.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.107285 restraints weight = 14438.601| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14502 Z= 0.221 Angle : 0.667 10.634 19647 Z= 0.336 Chirality : 0.043 0.190 2358 Planarity : 0.005 0.045 2427 Dihedral : 5.641 34.902 2805 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.64 % Allowed : 16.77 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1653 helix: 0.91 (0.26), residues: 405 sheet: 0.25 (0.29), residues: 315 loop : -0.73 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 28 HIS 0.006 0.001 HIS I 27 PHE 0.019 0.002 PHE B 522 TYR 0.011 0.002 TYR G 40 ARG 0.009 0.001 ARG I 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.16 seconds wall clock time: 49 minutes 43.47 seconds (2983.47 seconds total)