Starting phenix.real_space_refine on Sat Mar 16 12:26:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/03_2024/6x5c_22049_updated.pdb" } resolution = 4.04 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= 0.004 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 93 5.16 5 C 9212 2.51 5 N 2508 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "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 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "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 PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14644 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2745 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain breaks: 5 Chain: "B" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "C" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "D" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2752 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain breaks: 5 Chain: "F" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1156 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "I" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2719 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 20, 'TRANS': 326} Chain breaks: 5 Chain: "G" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1176 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "J" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" 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: "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: "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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UOV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.58 Number of scatterers: 14644 At special positions: 0 Unit cell: (152.95, 143.75, 109.25, 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 93 16.00 O 2831 8.00 N 2508 7.00 C 9212 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=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.02 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=2.02 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=2.08 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 84 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.07 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=2.03 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=2.03 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 F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 16 " - pdb=" SG CYS I 84 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.06 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.09 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 84 " distance=2.02 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 H 4 " - " MAN H 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " 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-ASN " NAG A 601 " - " ASN A 241 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 362 " " NAG A 611 " - " ASN A 386 " " NAG A 612 " - " ASN A 413 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 234 " " NAG D 601 " - " ASN D 241 " " NAG D 607 " - " ASN D 276 " " NAG D 608 " - " ASN D 295 " " NAG D 609 " - " ASN D 332 " " NAG D 610 " - " ASN D 362 " " NAG D 611 " - " ASN D 386 " " NAG D 612 " - " ASN D 413 " " NAG D 613 " - " ASN D 448 " " NAG E 608 " - " ASN E 276 " " NAG E 609 " - " ASN E 295 " " NAG E 610 " - " ASN E 332 " " NAG E 611 " - " ASN E 386 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG H 1 " - " ASN A 262 " " NAG K 1 " - " ASN D 262 " " NAG L 1 " - " ASN E 241 " " NAG M 1 " - " ASN E 262 " Time building additional restraints: 6.25 Conformation dependent library (CDL) restraints added in 2.8 seconds 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 27 sheets defined 25.9% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.659A 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 475 through 485 removed outlier: 4.029A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 521 No H-bonds generated for 'chain 'B' and resid 518 through 521' Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'B' and resid 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 567 through 596 removed outlier: 3.960A pdb=" N TRP B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.243A pdb=" N LYS B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 5.156A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 643 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 4.520A 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 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 335 through 352 removed outlier: 4.056A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (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 475 through 482 removed outlier: 3.620A pdb=" N ARG D 480 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 525 removed outlier: 3.890A pdb=" N GLY F 524 " --> pdb=" O LEU F 520 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA F 525 " --> pdb=" O GLY F 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 520 through 525' Processing helix chain 'F' and resid 530 through 545 Processing helix chain 'F' and resid 562 through 564 No H-bonds generated for 'chain 'F' and resid 562 through 564' Processing helix chain 'F' and resid 567 through 596 removed outlier: 3.969A pdb=" N TRP F 571 " --> pdb=" O GLN F 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 614 No H-bonds generated for 'chain 'F' and resid 612 through 614' Processing helix chain 'F' and resid 619 through 625 Processing helix chain 'F' and resid 628 through 634 removed outlier: 4.252A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 658 removed outlier: 5.220A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 4.914A 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 helix chain 'E' and resid 65 through 72 removed outlier: 3.832A pdb=" N HIS E 72 " --> pdb=" O VAL E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 113 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.002A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 478 through 485 removed outlier: 3.626A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 521 through 527 removed outlier: 3.954A pdb=" N GLY G 527 " --> pdb=" O LEU G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 545 Processing helix chain 'G' and resid 562 through 564 No H-bonds generated for 'chain 'G' and resid 562 through 564' Processing helix chain 'G' and resid 568 through 596 removed outlier: 4.881A pdb=" N GLY G 594 " --> pdb=" O GLN G 590 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE G 595 " --> pdb=" O GLN G 591 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 628 through 634 removed outlier: 4.129A pdb=" N LYS G 633 " --> pdb=" O MET G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 636 through 657 removed outlier: 5.323A pdb=" N GLN G 640 " --> pdb=" O ASN G 637 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR G 643 " --> pdb=" O GLN G 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 64 removed outlier: 4.194A pdb=" N ASP J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 78 No H-bonds generated for 'chain 'J' and resid 76 through 78' Processing sheet with id= A, first strand: chain 'A' and resid 34 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 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 199 through 202 Processing sheet with id= F, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.597A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 443 through 449 Processing sheet with id= H, first strand: chain 'C' and resid 2 through 5 removed outlier: 5.292A pdb=" N PHE C 26 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN C 30 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS C 35 " --> pdb=" O ASN C 30 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 12 through 17 Processing sheet with id= J, first strand: chain 'D' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= M, first strand: chain 'D' and resid 199 through 202 Processing sheet with id= N, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.630A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 447 through 449 removed outlier: 3.562A pdb=" N GLN D 417 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 2 through 5 removed outlier: 3.589A pdb=" N LYS I 2 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE I 26 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN I 30 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS I 35 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 14 through 17 Processing sheet with id= R, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= S, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= T, first strand: chain 'E' and resid 53 through 56 Processing sheet with id= U, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= V, first strand: chain 'E' and resid 199 through 202 Processing sheet with id= W, first strand: chain 'E' and resid 242 through 245 Processing sheet with id= X, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= Y, first strand: chain 'E' and resid 443 through 449 removed outlier: 3.518A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 2 through 5 removed outlier: 3.590A pdb=" N LYS J 2 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE J 26 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU J 37 " --> pdb=" O TRP J 28 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASN J 30 " --> pdb=" O LYS J 35 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS J 35 " --> pdb=" O ASN J 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY J 38 " --> pdb=" O THR J 45 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 12 through 17 516 hydrogen bonds defined for protein. 1215 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: 4.83 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2719 1.32 - 1.45: 4574 1.45 - 1.59: 7424 1.59 - 1.73: 83 1.73 - 1.86: 124 Bond restraints: 14924 Sorted by residual: bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.56e+01 bond pdb=" CB HIS E 66 " pdb=" CG HIS E 66 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.40e+01 bond pdb=" C15 UOV G 800 " pdb=" C16 UOV G 800 " ideal model delta sigma weight residual 1.474 1.603 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" CB ASP J 63 " pdb=" CG ASP J 63 " ideal model delta sigma weight residual 1.516 1.676 -0.160 2.50e-02 1.60e+03 4.10e+01 ... (remaining 14919 not shown) Histogram of bond angle deviations from ideal: 84.48 - 94.56: 9 94.56 - 104.64: 254 104.64 - 114.72: 9168 114.72 - 124.80: 10251 124.80 - 134.87: 550 Bond angle restraints: 20232 Sorted by residual: angle pdb=" N VAL I 12 " pdb=" CA VAL I 12 " pdb=" C VAL I 12 " ideal model delta sigma weight residual 110.82 121.89 -11.07 9.70e-01 1.06e+00 1.30e+02 angle pdb=" C08 UOV G 800 " pdb=" C09 UOV G 800 " pdb=" N10 UOV G 800 " ideal model delta sigma weight residual 97.96 128.48 -30.52 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C15 UOV F 800 " pdb=" C16 UOV F 800 " pdb=" O19 UOV F 800 " ideal model delta sigma weight residual 96.48 123.63 -27.15 3.00e+00 1.11e-01 8.19e+01 angle pdb=" C15 UOV G 800 " pdb=" C16 UOV G 800 " pdb=" O19 UOV G 800 " ideal model delta sigma weight residual 96.48 123.08 -26.60 3.00e+00 1.11e-01 7.86e+01 angle pdb=" C15 UOV B 800 " pdb=" C16 UOV B 800 " pdb=" O19 UOV B 800 " ideal model delta sigma weight residual 96.48 122.93 -26.45 3.00e+00 1.11e-01 7.77e+01 ... (remaining 20227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.83: 9260 23.83 - 47.67: 161 47.67 - 71.50: 81 71.50 - 95.33: 19 95.33 - 119.16: 27 Dihedral angle restraints: 9548 sinusoidal: 4430 harmonic: 5118 Sorted by residual: 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 -166.36 80.36 1 1.00e+01 1.00e-02 7.99e+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 -163.21 77.21 1 1.00e+01 1.00e-02 7.48e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -163.05 77.05 1 1.00e+01 1.00e-02 7.45e+01 ... (remaining 9545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1679 0.110 - 0.220: 510 0.220 - 0.329: 119 0.329 - 0.439: 60 0.439 - 0.549: 18 Chirality restraints: 2386 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.67e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.66e+01 ... (remaining 2383 not shown) Planarity restraints: 2553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 392 " -0.071 2.00e-02 2.50e+03 7.49e-02 7.01e+01 pdb=" CG ASN E 392 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN E 392 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 392 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG E 612 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.069 2.00e-02 2.50e+03 7.11e-02 6.32e+01 pdb=" CG ASN A 234 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.109 2.00e-02 2.50e+03 pdb=" C1 NAG A 614 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 241 " -0.059 2.00e-02 2.50e+03 6.22e-02 4.84e+01 pdb=" CG ASN A 241 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 241 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 241 " 0.095 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.077 2.00e-02 2.50e+03 ... (remaining 2550 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5843 2.91 - 3.41: 13684 3.41 - 3.90: 24979 3.90 - 4.40: 29217 4.40 - 4.90: 45782 Nonbonded interactions: 119505 Sorted by model distance: nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 121 " model vdw 2.409 2.520 nonbonded pdb=" NZ LYS E 231 " pdb=" OE1 GLU E 267 " model vdw 2.411 2.520 nonbonded pdb=" NZ LYS D 231 " pdb=" OE1 GLU D 267 " model vdw 2.420 2.520 nonbonded pdb=" OD1 ASP D 113 " pdb=" NZ LYS D 121 " model vdw 2.426 2.520 nonbonded pdb=" N ASN A 301 " pdb=" N ASN A 302 " model vdw 2.429 2.560 ... (remaining 119500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 124 or resid 197 through 305 or resid 325 throu \ gh 353 or resid 362 through 457 or resid 468 through 504 or resid 601 through 61 \ 1)) selection = (chain 'D' and (resid 33 through 124 or resid 197 through 353 or resid 362 throu \ gh 504 or resid 601 through 611)) selection = (chain 'E' and (resid 33 through 305 or resid 325 through 457 or resid 468 throu \ gh 504 or resid 608 through 613)) } ncs_group { reference = (chain 'B' and (resid 517 through 659 or resid 800)) selection = (chain 'F' and (resid 517 through 659 or resid 800)) selection = (chain 'G' and (resid 517 through 659 or resid 800)) } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.760 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.120 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.021 0.160 14924 Z= 1.364 Angle : 1.820 30.518 20232 Z= 1.163 Chirality : 0.129 0.549 2386 Planarity : 0.009 0.041 2526 Dihedral : 13.283 119.165 6128 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.24 (0.19), residues: 1728 helix: 0.04 (0.24), residues: 423 sheet: 0.61 (0.26), residues: 383 loop : 0.16 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.010 TRP E 479 HIS 0.013 0.002 HIS A 72 PHE 0.036 0.007 PHE D 382 TYR 0.047 0.008 TYR B 638 ARG 0.007 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.776 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: A 421 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7301 (mmtt) REVERT: A 434 MET cc_start: 0.6612 (tmm) cc_final: 0.5435 (mtt) REVERT: B 567 GLN cc_start: 0.8014 (tp40) cc_final: 0.7766 (tm-30) REVERT: C 34 ILE cc_start: 0.8180 (mm) cc_final: 0.7850 (mm) REVERT: C 83 ILE cc_start: 0.5422 (tp) cc_final: 0.5211 (tp) REVERT: D 35 TRP cc_start: 0.6836 (m100) cc_final: 0.6599 (m100) REVERT: D 62 ASP cc_start: 0.5790 (p0) cc_final: 0.5490 (t0) REVERT: D 104 MET cc_start: 0.8686 (ttt) cc_final: 0.8430 (tpp) REVERT: D 260 LEU cc_start: 0.7283 (mt) cc_final: 0.6934 (tp) REVERT: D 279 ASP cc_start: 0.7906 (p0) cc_final: 0.7324 (t70) REVERT: D 416 LEU cc_start: 0.8742 (mt) cc_final: 0.8442 (mp) REVERT: I 67 PHE cc_start: 0.8356 (m-80) cc_final: 0.7447 (m-10) REVERT: I 70 ILE cc_start: 0.7902 (mt) cc_final: 0.7231 (mm) REVERT: I 73 ASN cc_start: 0.8481 (t0) cc_final: 0.7773 (t0) REVERT: I 89 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7099 (mp10) REVERT: E 40 TYR cc_start: 0.8240 (t80) cc_final: 0.7969 (t80) REVERT: E 96 TRP cc_start: 0.8227 (m-90) cc_final: 0.7998 (m-10) REVERT: E 97 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8503 (mtmt) REVERT: G 548 ILE cc_start: 0.9013 (mt) cc_final: 0.8795 (tp) REVERT: J 13 GLU cc_start: 0.4638 (tt0) cc_final: 0.3786 (pp20) REVERT: J 86 VAL cc_start: 0.7663 (t) cc_final: 0.7355 (p) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2950 time to fit residues: 182.3307 Evaluate side-chains 203 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN D 229 ASN E 352 GLN G 652 GLN J 33 GLN J 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14924 Z= 0.281 Angle : 0.765 15.914 20232 Z= 0.397 Chirality : 0.049 0.191 2386 Planarity : 0.005 0.054 2526 Dihedral : 11.841 116.444 2703 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.06 % Allowed : 1.53 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1728 helix: 0.16 (0.25), residues: 429 sheet: 0.35 (0.27), residues: 360 loop : -0.15 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 28 HIS 0.009 0.002 HIS A 66 PHE 0.016 0.002 PHE A 383 TYR 0.033 0.003 TYR D 484 ARG 0.007 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.661 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: A 64 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 421 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7776 (mmtt) REVERT: A 434 MET cc_start: 0.6348 (tmm) cc_final: 0.5249 (mtt) REVERT: B 584 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8366 (mt-10) REVERT: B 629 MET cc_start: 0.7696 (mmm) cc_final: 0.7424 (tpt) REVERT: B 657 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7710 (tm-30) REVERT: D 35 TRP cc_start: 0.6849 (m100) cc_final: 0.6507 (m100) REVERT: D 279 ASP cc_start: 0.7498 (p0) cc_final: 0.7229 (t70) REVERT: D 488 VAL cc_start: 0.8822 (t) cc_final: 0.8535 (p) REVERT: F 539 VAL cc_start: 0.8906 (t) cc_final: 0.8568 (p) REVERT: I 67 PHE cc_start: 0.8204 (m-80) cc_final: 0.7172 (m-10) REVERT: I 73 ASN cc_start: 0.8537 (t0) cc_final: 0.8034 (t0) REVERT: I 94 GLN cc_start: 0.8537 (tt0) cc_final: 0.8333 (tt0) REVERT: E 96 TRP cc_start: 0.8234 (m-90) cc_final: 0.7968 (m-10) REVERT: E 97 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8446 (mmtp) REVERT: G 570 VAL cc_start: 0.8462 (m) cc_final: 0.8006 (t) REVERT: G 618 THR cc_start: 0.8012 (p) cc_final: 0.7764 (p) REVERT: J 13 GLU cc_start: 0.5443 (tt0) cc_final: 0.4331 (pp20) REVERT: J 66 ASN cc_start: 0.8745 (t0) cc_final: 0.8524 (t0) outliers start: 1 outliers final: 1 residues processed: 290 average time/residue: 0.2458 time to fit residues: 106.4327 Evaluate side-chains 175 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 170 optimal weight: 0.0070 chunk 140 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14924 Z= 0.211 Angle : 0.668 16.046 20232 Z= 0.340 Chirality : 0.046 0.166 2386 Planarity : 0.005 0.045 2526 Dihedral : 10.857 113.499 2703 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 0.06 % Allowed : 1.66 % Favored : 98.27 % 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: -0.19 (0.20), residues: 1728 helix: 0.07 (0.26), residues: 423 sheet: 0.24 (0.27), residues: 346 loop : -0.26 (0.20), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 45 HIS 0.015 0.002 HIS C 27 PHE 0.015 0.002 PHE F 522 TYR 0.032 0.002 TYR D 484 ARG 0.006 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 261 time to evaluate : 1.706 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: A 113 ASP cc_start: 0.9015 (t70) cc_final: 0.8661 (t0) REVERT: A 201 ILE cc_start: 0.8979 (pt) cc_final: 0.8774 (pt) REVERT: A 421 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7899 (mmtt) REVERT: A 434 MET cc_start: 0.6426 (tmm) cc_final: 0.4871 (mtt) REVERT: C 44 LEU cc_start: 0.7765 (tp) cc_final: 0.7519 (tp) REVERT: D 35 TRP cc_start: 0.6860 (m100) cc_final: 0.6470 (m100) REVERT: D 279 ASP cc_start: 0.7717 (p0) cc_final: 0.7092 (t70) REVERT: F 539 VAL cc_start: 0.8872 (t) cc_final: 0.8642 (p) REVERT: I 66 ASN cc_start: 0.8655 (m110) cc_final: 0.8450 (m110) REVERT: I 67 PHE cc_start: 0.8163 (m-80) cc_final: 0.7623 (m-10) REVERT: I 73 ASN cc_start: 0.8644 (t0) cc_final: 0.8139 (t0) REVERT: E 97 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8418 (mmtp) REVERT: E 203 GLN cc_start: 0.8662 (mt0) cc_final: 0.8093 (mp-120) REVERT: G 542 ARG cc_start: 0.8248 (ptt180) cc_final: 0.7978 (ttm170) REVERT: G 570 VAL cc_start: 0.8476 (m) cc_final: 0.7978 (t) REVERT: G 585 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8359 (mtm110) REVERT: G 621 GLU cc_start: 0.8330 (pt0) cc_final: 0.8035 (pt0) REVERT: J 13 GLU cc_start: 0.5169 (tt0) cc_final: 0.4524 (pp20) REVERT: J 56 ASP cc_start: 0.7898 (p0) cc_final: 0.7605 (p0) REVERT: J 66 ASN cc_start: 0.8742 (t0) cc_final: 0.8481 (t0) REVERT: J 94 GLN cc_start: 0.6644 (tt0) cc_final: 0.5933 (tp-100) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.2374 time to fit residues: 93.8938 Evaluate side-chains 178 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 363 HIS ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 540 GLN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN J 32 ASN J 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14924 Z= 0.351 Angle : 0.757 14.627 20232 Z= 0.383 Chirality : 0.050 0.209 2386 Planarity : 0.005 0.055 2526 Dihedral : 10.606 114.806 2703 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % 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: -0.63 (0.20), residues: 1728 helix: -0.22 (0.25), residues: 414 sheet: 0.05 (0.27), residues: 377 loop : -0.63 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 96 HIS 0.009 0.002 HIS A 374 PHE 0.024 0.003 PHE G 522 TYR 0.036 0.003 TYR D 484 ARG 0.007 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.848 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 113 ASP cc_start: 0.9058 (t70) cc_final: 0.8701 (t0) REVERT: A 434 MET cc_start: 0.6806 (tmm) cc_final: 0.5886 (mtt) REVERT: C 44 LEU cc_start: 0.7733 (tp) cc_final: 0.7427 (tp) REVERT: D 35 TRP cc_start: 0.6963 (m100) cc_final: 0.6574 (m100) REVERT: D 279 ASP cc_start: 0.8086 (p0) cc_final: 0.7352 (t0) REVERT: D 475 MET cc_start: 0.8175 (mmm) cc_final: 0.7772 (mmm) REVERT: F 519 ILE cc_start: 0.9201 (mp) cc_final: 0.8964 (tp) REVERT: F 567 GLN cc_start: 0.8979 (tp40) cc_final: 0.8362 (tm-30) REVERT: I 66 ASN cc_start: 0.8838 (m110) cc_final: 0.8563 (m110) REVERT: I 67 PHE cc_start: 0.8234 (m-80) cc_final: 0.7145 (m-10) REVERT: I 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8219 (t0) REVERT: E 97 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8373 (mmtp) REVERT: E 203 GLN cc_start: 0.8879 (mt0) cc_final: 0.8295 (mp-120) REVERT: G 542 ARG cc_start: 0.8313 (ptt180) cc_final: 0.7957 (ttm170) REVERT: J 13 GLU cc_start: 0.4530 (tt0) cc_final: 0.3951 (pp20) REVERT: J 33 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8381 (tm-30) REVERT: J 82 TYR cc_start: 0.5756 (m-80) cc_final: 0.5516 (m-80) REVERT: J 94 GLN cc_start: 0.6941 (tt0) cc_final: 0.6414 (tp40) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.2486 time to fit residues: 87.9064 Evaluate side-chains 164 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN F 551 GLN F 652 GLN F 656 ASN E 103 GLN E 246 GLN G 564 HIS G 640 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14924 Z= 0.227 Angle : 0.665 13.733 20232 Z= 0.334 Chirality : 0.046 0.195 2386 Planarity : 0.005 0.054 2526 Dihedral : 10.143 111.445 2703 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.06 % Allowed : 1.60 % Favored : 98.34 % 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: -0.67 (0.20), residues: 1728 helix: -0.05 (0.26), residues: 416 sheet: 0.01 (0.27), residues: 369 loop : -0.77 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 96 HIS 0.007 0.001 HIS C 27 PHE 0.015 0.002 PHE D 233 TYR 0.031 0.002 TYR D 484 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9098 (t70) cc_final: 0.8754 (t0) REVERT: A 434 MET cc_start: 0.7014 (tmm) cc_final: 0.6073 (mtt) REVERT: C 20 GLN cc_start: 0.8451 (mp10) cc_final: 0.8041 (mp10) REVERT: D 35 TRP cc_start: 0.6835 (m100) cc_final: 0.6524 (m100) REVERT: D 104 MET cc_start: 0.8708 (tpp) cc_final: 0.8167 (tpp) REVERT: D 279 ASP cc_start: 0.7983 (p0) cc_final: 0.7215 (t70) REVERT: F 567 GLN cc_start: 0.8909 (tp40) cc_final: 0.8356 (tm-30) REVERT: I 66 ASN cc_start: 0.8813 (m110) cc_final: 0.8608 (m110) REVERT: I 67 PHE cc_start: 0.8163 (m-80) cc_final: 0.7125 (m-10) REVERT: I 73 ASN cc_start: 0.8662 (t0) cc_final: 0.8236 (t0) REVERT: E 80 ASN cc_start: 0.7960 (m-40) cc_final: 0.6666 (p0) REVERT: E 97 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8327 (mmtp) REVERT: E 203 GLN cc_start: 0.8880 (mt0) cc_final: 0.8397 (mp-120) REVERT: E 435 TYR cc_start: 0.6887 (m-80) cc_final: 0.6678 (m-10) REVERT: G 542 ARG cc_start: 0.8287 (ptt180) cc_final: 0.7893 (ttm170) REVERT: G 552 GLN cc_start: 0.6331 (tp40) cc_final: 0.6033 (mm-40) REVERT: G 581 LEU cc_start: 0.8356 (tp) cc_final: 0.8051 (tp) REVERT: J 13 GLU cc_start: 0.5661 (tt0) cc_final: 0.5338 (pp20) REVERT: J 56 ASP cc_start: 0.8024 (p0) cc_final: 0.7779 (p0) REVERT: J 66 ASN cc_start: 0.9077 (t0) cc_final: 0.8763 (t0) REVERT: J 82 TYR cc_start: 0.6067 (m-80) cc_final: 0.5801 (m-80) REVERT: J 90 LYS cc_start: 0.7791 (mttm) cc_final: 0.7487 (mmtm) REVERT: J 94 GLN cc_start: 0.6926 (tt0) cc_final: 0.6463 (tp40) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.2598 time to fit residues: 92.0383 Evaluate side-chains 167 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 374 HIS C 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14924 Z= 0.274 Angle : 0.696 13.060 20232 Z= 0.353 Chirality : 0.047 0.215 2386 Planarity : 0.005 0.058 2526 Dihedral : 10.214 114.499 2703 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.80 (0.20), residues: 1728 helix: -0.09 (0.26), residues: 419 sheet: 0.03 (0.28), residues: 370 loop : -0.93 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 96 HIS 0.008 0.002 HIS D 216 PHE 0.023 0.002 PHE G 522 TYR 0.031 0.003 TYR D 484 ARG 0.005 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9076 (t70) cc_final: 0.8731 (t0) REVERT: A 434 MET cc_start: 0.6993 (tmm) cc_final: 0.6087 (mtt) REVERT: D 35 TRP cc_start: 0.6932 (m100) cc_final: 0.6574 (m100) REVERT: D 104 MET cc_start: 0.8542 (ttt) cc_final: 0.8236 (tpp) REVERT: D 217 TYR cc_start: 0.7940 (m-80) cc_final: 0.6824 (m-80) REVERT: D 279 ASP cc_start: 0.8010 (p0) cc_final: 0.7262 (t70) REVERT: F 567 GLN cc_start: 0.8940 (tp40) cc_final: 0.8552 (tm-30) REVERT: I 58 ARG cc_start: 0.8598 (tpm170) cc_final: 0.8347 (tpm170) REVERT: I 66 ASN cc_start: 0.8863 (m110) cc_final: 0.8663 (m110) REVERT: I 67 PHE cc_start: 0.8220 (m-80) cc_final: 0.7128 (m-10) REVERT: I 73 ASN cc_start: 0.8639 (t0) cc_final: 0.8132 (t0) REVERT: E 80 ASN cc_start: 0.7982 (m-40) cc_final: 0.6653 (p0) REVERT: E 97 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8127 (mmtp) REVERT: E 203 GLN cc_start: 0.8914 (mt0) cc_final: 0.8450 (mp-120) REVERT: E 435 TYR cc_start: 0.6875 (m-80) cc_final: 0.6513 (m-10) REVERT: G 530 MET cc_start: 0.8051 (mtp) cc_final: 0.7601 (mtp) REVERT: G 552 GLN cc_start: 0.6244 (tp40) cc_final: 0.5952 (mm-40) REVERT: G 581 LEU cc_start: 0.8484 (tp) cc_final: 0.8152 (tp) REVERT: G 638 TYR cc_start: 0.7837 (m-80) cc_final: 0.7567 (m-10) REVERT: J 82 TYR cc_start: 0.6564 (m-80) cc_final: 0.6280 (m-80) REVERT: J 86 VAL cc_start: 0.7535 (t) cc_final: 0.7216 (p) REVERT: J 90 LYS cc_start: 0.7741 (mttm) cc_final: 0.7448 (mmtm) REVERT: J 94 GLN cc_start: 0.7084 (tt0) cc_final: 0.6518 (tp-100) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2538 time to fit residues: 89.7053 Evaluate side-chains 164 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN D 422 GLN ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN E 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 14924 Z= 0.366 Angle : 0.779 13.523 20232 Z= 0.394 Chirality : 0.050 0.222 2386 Planarity : 0.005 0.058 2526 Dihedral : 10.680 113.737 2703 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1728 helix: -0.29 (0.26), residues: 414 sheet: -0.12 (0.28), residues: 370 loop : -1.17 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP E 96 HIS 0.006 0.002 HIS J 27 PHE 0.034 0.002 PHE G 522 TYR 0.030 0.003 TYR D 484 ARG 0.007 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8165 (mmtt) REVERT: A 434 MET cc_start: 0.7068 (tmm) cc_final: 0.5759 (mtt) REVERT: D 35 TRP cc_start: 0.6907 (m100) cc_final: 0.6520 (m100) REVERT: D 104 MET cc_start: 0.8602 (ttt) cc_final: 0.8275 (tpp) REVERT: F 567 GLN cc_start: 0.8958 (tp40) cc_final: 0.8418 (tm-30) REVERT: F 629 MET cc_start: 0.8072 (mtp) cc_final: 0.7801 (mtp) REVERT: I 66 ASN cc_start: 0.8954 (m110) cc_final: 0.8718 (m110) REVERT: I 67 PHE cc_start: 0.8318 (m-80) cc_final: 0.7168 (m-10) REVERT: I 73 ASN cc_start: 0.8703 (t0) cc_final: 0.8259 (t0) REVERT: E 80 ASN cc_start: 0.7910 (m110) cc_final: 0.6932 (p0) REVERT: E 97 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8122 (mmtm) REVERT: E 203 GLN cc_start: 0.8965 (mt0) cc_final: 0.8499 (mp-120) REVERT: E 435 TYR cc_start: 0.6784 (m-80) cc_final: 0.6182 (m-80) REVERT: E 475 MET cc_start: 0.8589 (mmt) cc_final: 0.8180 (mmt) REVERT: G 552 GLN cc_start: 0.6280 (tp40) cc_final: 0.5990 (mm-40) REVERT: G 638 TYR cc_start: 0.7904 (m-80) cc_final: 0.7649 (m-10) REVERT: J 56 ASP cc_start: 0.8069 (p0) cc_final: 0.7865 (p0) REVERT: J 82 TYR cc_start: 0.6570 (m-80) cc_final: 0.6332 (m-80) REVERT: J 86 VAL cc_start: 0.7597 (t) cc_final: 0.7254 (p) REVERT: J 90 LYS cc_start: 0.7942 (mttm) cc_final: 0.7532 (mmtm) REVERT: J 94 GLN cc_start: 0.7101 (tt0) cc_final: 0.6695 (tp40) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.2356 time to fit residues: 78.3990 Evaluate side-chains 160 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS B 562 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 105 HIS E 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14924 Z= 0.234 Angle : 0.688 12.942 20232 Z= 0.346 Chirality : 0.047 0.362 2386 Planarity : 0.005 0.060 2526 Dihedral : 10.242 111.984 2703 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1728 helix: -0.10 (0.26), residues: 406 sheet: -0.08 (0.28), residues: 378 loop : -1.11 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.002 TRP E 96 HIS 0.005 0.001 HIS A 374 PHE 0.018 0.002 PHE G 522 TYR 0.025 0.002 TYR D 484 ARG 0.004 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.7070 (tmm) cc_final: 0.6052 (mtt) REVERT: B 626 MET cc_start: 0.7294 (ttm) cc_final: 0.6809 (ttm) REVERT: D 35 TRP cc_start: 0.6716 (m100) cc_final: 0.6339 (m-10) REVERT: D 217 TYR cc_start: 0.7779 (m-80) cc_final: 0.7250 (m-80) REVERT: F 567 GLN cc_start: 0.8924 (tp40) cc_final: 0.8396 (tm-30) REVERT: F 620 ASN cc_start: 0.8925 (m-40) cc_final: 0.8694 (t0) REVERT: F 629 MET cc_start: 0.8007 (mtp) cc_final: 0.7694 (mtp) REVERT: I 66 ASN cc_start: 0.8951 (m110) cc_final: 0.8692 (m110) REVERT: I 67 PHE cc_start: 0.8290 (m-80) cc_final: 0.7163 (m-10) REVERT: I 73 ASN cc_start: 0.8689 (t0) cc_final: 0.8256 (t0) REVERT: E 80 ASN cc_start: 0.7865 (m110) cc_final: 0.7091 (p0) REVERT: E 203 GLN cc_start: 0.8907 (mt0) cc_final: 0.8516 (mp-120) REVERT: E 435 TYR cc_start: 0.6699 (m-80) cc_final: 0.6133 (m-80) REVERT: G 530 MET cc_start: 0.7962 (mtp) cc_final: 0.7287 (mtp) REVERT: G 552 GLN cc_start: 0.6215 (tp40) cc_final: 0.5943 (mm-40) REVERT: G 565 MET cc_start: 0.8036 (ttm) cc_final: 0.7702 (ttt) REVERT: G 638 TYR cc_start: 0.7862 (m-80) cc_final: 0.7613 (m-10) REVERT: J 82 TYR cc_start: 0.6458 (m-80) cc_final: 0.6230 (m-80) REVERT: J 86 VAL cc_start: 0.7570 (t) cc_final: 0.7246 (p) REVERT: J 90 LYS cc_start: 0.7957 (mttm) cc_final: 0.7522 (mmtm) REVERT: J 94 GLN cc_start: 0.7150 (tt0) cc_final: 0.6686 (tp-100) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2537 time to fit residues: 82.0675 Evaluate side-chains 164 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 0.0470 chunk 140 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN E 99 ASN E 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14924 Z= 0.236 Angle : 0.685 12.944 20232 Z= 0.346 Chirality : 0.047 0.287 2386 Planarity : 0.005 0.061 2526 Dihedral : 10.073 113.809 2703 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.98 (0.20), residues: 1728 helix: -0.11 (0.26), residues: 412 sheet: -0.11 (0.27), residues: 395 loop : -1.13 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.141 0.002 TRP E 96 HIS 0.004 0.001 HIS A 66 PHE 0.019 0.002 PHE A 233 TYR 0.022 0.002 TYR D 484 ARG 0.004 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 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: A 80 ASN cc_start: 0.8012 (t0) cc_final: 0.7398 (p0) REVERT: A 426 MET cc_start: 0.8553 (tpp) cc_final: 0.8273 (mmm) REVERT: A 434 MET cc_start: 0.7071 (tmm) cc_final: 0.6174 (mtt) REVERT: B 540 GLN cc_start: 0.8883 (mm110) cc_final: 0.8543 (pp30) REVERT: B 626 MET cc_start: 0.7298 (ttm) cc_final: 0.6883 (ttm) REVERT: D 35 TRP cc_start: 0.6742 (m100) cc_final: 0.6357 (m-10) REVERT: D 104 MET cc_start: 0.8586 (tpp) cc_final: 0.7969 (tpp) REVERT: D 217 TYR cc_start: 0.7731 (m-80) cc_final: 0.7239 (m-80) REVERT: F 567 GLN cc_start: 0.8979 (tp40) cc_final: 0.8436 (tm-30) REVERT: F 620 ASN cc_start: 0.8945 (m-40) cc_final: 0.8706 (t0) REVERT: F 629 MET cc_start: 0.8055 (mtp) cc_final: 0.7322 (mtt) REVERT: I 28 TRP cc_start: 0.7427 (m100) cc_final: 0.6903 (m100) REVERT: I 66 ASN cc_start: 0.8992 (m110) cc_final: 0.8736 (m110) REVERT: I 67 PHE cc_start: 0.8307 (m-80) cc_final: 0.7195 (m-10) REVERT: I 73 ASN cc_start: 0.8574 (t0) cc_final: 0.8088 (t0) REVERT: E 80 ASN cc_start: 0.7916 (m110) cc_final: 0.7234 (p0) REVERT: E 203 GLN cc_start: 0.8881 (mt0) cc_final: 0.8571 (mp-120) REVERT: E 435 TYR cc_start: 0.6722 (m-80) cc_final: 0.6130 (m-80) REVERT: G 530 MET cc_start: 0.8020 (mtp) cc_final: 0.7217 (mtp) REVERT: G 552 GLN cc_start: 0.6416 (tp40) cc_final: 0.6052 (mm-40) REVERT: G 638 TYR cc_start: 0.7857 (m-80) cc_final: 0.7598 (m-10) REVERT: J 82 TYR cc_start: 0.6592 (m-80) cc_final: 0.6345 (m-80) REVERT: J 86 VAL cc_start: 0.7594 (t) cc_final: 0.7277 (p) REVERT: J 94 GLN cc_start: 0.7158 (tt0) cc_final: 0.6664 (tp-100) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2498 time to fit residues: 84.0487 Evaluate side-chains 166 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** B 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 ASN E 99 ASN E 105 HIS E 417 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14924 Z= 0.317 Angle : 0.744 13.863 20232 Z= 0.375 Chirality : 0.048 0.255 2386 Planarity : 0.005 0.065 2526 Dihedral : 10.381 114.612 2703 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.18 (0.20), residues: 1728 helix: -0.22 (0.26), residues: 411 sheet: -0.18 (0.28), residues: 375 loop : -1.28 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.159 0.003 TRP E 96 HIS 0.008 0.002 HIS A 374 PHE 0.033 0.002 PHE G 522 TYR 0.034 0.003 TYR A 40 ARG 0.006 0.001 ARG A 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8583 (tpp) cc_final: 0.8253 (mmm) REVERT: A 434 MET cc_start: 0.7122 (tmm) cc_final: 0.6117 (mtt) REVERT: B 626 MET cc_start: 0.7504 (ttm) cc_final: 0.6954 (ttm) REVERT: C 20 GLN cc_start: 0.8503 (mp10) cc_final: 0.8177 (mp10) REVERT: D 35 TRP cc_start: 0.6717 (m100) cc_final: 0.6357 (m100) REVERT: D 104 MET cc_start: 0.8549 (tpp) cc_final: 0.8067 (tpp) REVERT: F 567 GLN cc_start: 0.8950 (tp40) cc_final: 0.8318 (tm-30) REVERT: F 620 ASN cc_start: 0.8977 (m-40) cc_final: 0.8750 (t0) REVERT: F 629 MET cc_start: 0.8028 (mtp) cc_final: 0.7715 (mtp) REVERT: I 66 ASN cc_start: 0.9036 (m110) cc_final: 0.8790 (m110) REVERT: I 67 PHE cc_start: 0.8336 (m-80) cc_final: 0.7276 (m-10) REVERT: I 73 ASN cc_start: 0.8508 (t0) cc_final: 0.8047 (t0) REVERT: E 80 ASN cc_start: 0.7887 (m110) cc_final: 0.7290 (p0) REVERT: E 97 LYS cc_start: 0.8570 (mmtt) cc_final: 0.7923 (mmtm) REVERT: E 203 GLN cc_start: 0.8936 (mt0) cc_final: 0.8630 (mp-120) REVERT: E 435 TYR cc_start: 0.6740 (m-80) cc_final: 0.6154 (m-80) REVERT: G 530 MET cc_start: 0.8154 (mtp) cc_final: 0.7273 (mtp) REVERT: G 552 GLN cc_start: 0.6509 (tp40) cc_final: 0.6159 (mm-40) REVERT: J 86 VAL cc_start: 0.7767 (t) cc_final: 0.7417 (p) REVERT: J 94 GLN cc_start: 0.7361 (tt0) cc_final: 0.6855 (tp-100) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2224 time to fit residues: 71.9675 Evaluate side-chains 156 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 105 HIS E 417 GLN J 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.112075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.098337 restraints weight = 44388.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.100643 restraints weight = 26219.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.102148 restraints weight = 17564.234| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14924 Z= 0.234 Angle : 0.683 12.880 20232 Z= 0.342 Chirality : 0.046 0.246 2386 Planarity : 0.005 0.065 2526 Dihedral : 10.078 112.875 2703 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -1.06 (0.20), residues: 1728 helix: -0.01 (0.26), residues: 400 sheet: -0.19 (0.27), residues: 401 loop : -1.23 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.002 TRP E 96 HIS 0.004 0.001 HIS A 66 PHE 0.018 0.002 PHE G 522 TYR 0.018 0.002 TYR A 40 ARG 0.005 0.000 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.69 seconds wall clock time: 51 minutes 56.15 seconds (3116.15 seconds total)