Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 13:43:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_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_22049/07_2023/6x5c_22049_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x5c_22049/07_2023/6x5c_22049_updated.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 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 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 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 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 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 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 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: 6.87, per 1000 atoms: 0.47 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: 5.69 Conformation dependent library (CDL) restraints added in 2.0 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: 1.37 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: 4.87 Time building geometry restraints manager: 6.18 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: 8486 23.83 - 47.67: 145 47.67 - 71.50: 73 71.50 - 95.33: 7 95.33 - 119.16: 15 Dihedral angle restraints: 8726 sinusoidal: 3608 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 8723 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.720 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 37.120 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.150 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.060 ------------------------------------------------------------------------------- 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 : 12.195 119.165 5306 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 % 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 *********************** 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 : 1.677 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 outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3064 time to fit residues: 190.8518 Evaluate side-chains 193 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0813 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN J 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 14924 Z= 0.269 Angle : 0.762 16.153 20232 Z= 0.394 Chirality : 0.048 0.196 2386 Planarity : 0.005 0.053 2526 Dihedral : 10.736 117.075 1881 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.06 % 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: -0.03 (0.19), residues: 1728 helix: 0.12 (0.25), residues: 429 sheet: 0.40 (0.27), residues: 360 loop : -0.14 (0.19), residues: 939 *********************** 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 288 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.765 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 outliers start: 1 outliers final: 1 residues processed: 287 average time/residue: 0.2603 time to fit residues: 113.4653 Evaluate side-chains 167 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1692 time to fit residues: 2.5503 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 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 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: 0.7374 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 14924 Z= 0.243 Angle : 0.685 16.060 20232 Z= 0.350 Chirality : 0.046 0.175 2386 Planarity : 0.005 0.051 2526 Dihedral : 10.804 113.359 1881 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer Outliers : 0.06 % 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: 1728 helix: -0.01 (0.26), residues: 423 sheet: 0.27 (0.28), residues: 350 loop : -0.29 (0.20), residues: 955 *********************** 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 258 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.556 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 outliers start: 1 outliers final: 1 residues processed: 257 average time/residue: 0.2386 time to fit residues: 93.6665 Evaluate side-chains 166 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1688 time to fit residues: 2.7128 ------------------------------------------------------------------------------- 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: 5.9990 chunk 81 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 52 ASN F 551 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 540 GLN ** G 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN G 640 GLN J 32 ASN J 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 14924 Z= 0.369 Angle : 0.780 13.883 20232 Z= 0.396 Chirality : 0.050 0.231 2386 Planarity : 0.006 0.060 2526 Dihedral : 11.176 114.632 1881 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.19 % 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: -0.76 (0.20), residues: 1728 helix: -0.28 (0.25), residues: 416 sheet: -0.00 (0.27), residues: 386 loop : -0.76 (0.19), residues: 926 *********************** 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 230 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.2458 time to fit residues: 86.3669 Evaluate side-chains 158 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3737 ------------------------------------------------------------------------------- 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: 6.9990 chunk 94 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 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 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN F 656 ASN E 72 HIS E 103 GLN E 246 GLN G 564 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5132 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= 0.256 Angle : 0.713 19.274 20232 Z= 0.358 Chirality : 0.047 0.267 2386 Planarity : 0.005 0.052 2526 Dihedral : 10.967 111.855 1881 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.06 % 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: -0.79 (0.20), residues: 1728 helix: -0.02 (0.26), residues: 408 sheet: -0.06 (0.28), residues: 360 loop : -0.91 (0.19), residues: 960 *********************** 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 233 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.2656 time to fit residues: 92.4906 Evaluate side-chains 156 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1867 time to fit residues: 2.4820 ------------------------------------------------------------------------------- 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: 8.9990 chunk 150 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS G 652 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 14924 Z= 0.297 Angle : 0.734 13.226 20232 Z= 0.370 Chirality : 0.048 0.216 2386 Planarity : 0.005 0.050 2526 Dihedral : 11.015 114.528 1881 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.97 % Rotamer Outliers : 0.00 % 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: -0.85 (0.20), residues: 1728 helix: 0.09 (0.26), residues: 403 sheet: -0.06 (0.28), residues: 368 loop : -1.03 (0.19), residues: 957 *********************** 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 230 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2511 time to fit residues: 88.1351 Evaluate side-chains 155 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2149 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 422 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS G 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 14924 Z= 0.267 Angle : 0.714 13.514 20232 Z= 0.359 Chirality : 0.047 0.230 2386 Planarity : 0.005 0.057 2526 Dihedral : 10.936 112.087 1881 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer Outliers : 0.00 % 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: -0.98 (0.20), residues: 1728 helix: 0.03 (0.26), residues: 403 sheet: -0.22 (0.28), residues: 360 loop : -1.11 (0.19), residues: 965 *********************** 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 219 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2559 time to fit residues: 84.4954 Evaluate side-chains 159 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2903 ------------------------------------------------------------------------------- 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: 9.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 151 optimal weight: 0.0870 overall best weight: 1.7362 ------------------------------------------------------------------------------- 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 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 105 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS G 540 GLN G 564 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 14924 Z= 0.208 Angle : 0.685 13.206 20232 Z= 0.343 Chirality : 0.047 0.371 2386 Planarity : 0.004 0.056 2526 Dihedral : 10.789 112.717 1881 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.85 % Rotamer Outliers : 0.00 % 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: -0.98 (0.20), residues: 1728 helix: -0.04 (0.26), residues: 415 sheet: -0.09 (0.28), residues: 368 loop : -1.15 (0.19), residues: 945 *********************** 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 220 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2519 time to fit residues: 85.0179 Evaluate side-chains 155 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2861 ------------------------------------------------------------------------------- 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: 1.9990 chunk 145 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** D 352 GLN ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 105 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 GLN G 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 14924 Z= 0.273 Angle : 0.723 13.112 20232 Z= 0.365 Chirality : 0.048 0.297 2386 Planarity : 0.005 0.055 2526 Dihedral : 10.913 114.343 1881 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.00 % 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: -1.14 (0.20), residues: 1728 helix: -0.25 (0.26), residues: 415 sheet: -0.21 (0.27), residues: 383 loop : -1.22 (0.19), residues: 930 *********************** 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 204 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2458 time to fit residues: 77.5386 Evaluate side-chains 156 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2358 ------------------------------------------------------------------------------- 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: 0.0980 chunk 114 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN E 99 ASN E 105 HIS E 203 GLN E 417 GLN ** G 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 14924 Z= 0.234 Angle : 0.694 12.987 20232 Z= 0.349 Chirality : 0.047 0.269 2386 Planarity : 0.005 0.056 2526 Dihedral : 10.803 113.102 1881 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.13 % 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: -1.11 (0.20), residues: 1728 helix: -0.13 (0.26), residues: 411 sheet: -0.23 (0.27), residues: 394 loop : -1.23 (0.20), residues: 923 ********************** 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 209 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 209 average time/residue: 0.2549 time to fit residues: 80.8893 Evaluate side-chains 150 residues out of total 1564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1312 time to fit residues: 2.5469 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 120 optimal weight: 0.0570 overall best weight: 2.7304 ------------------------------------------------------------------------------- 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** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 105 HIS G 540 GLN G 552 GLN ** G 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.111345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097828 restraints weight = 44563.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.100066 restraints weight = 26433.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.101578 restraints weight = 17668.110| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 14924 Z= 0.268 Angle : 0.717 12.974 20232 Z= 0.362 Chirality : 0.048 0.240 2386 Planarity : 0.005 0.056 2526 Dihedral : 10.935 114.174 1881 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.00 % 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: -1.25 (0.20), residues: 1728 helix: -0.32 (0.25), residues: 418 sheet: -0.27 (0.26), residues: 408 loop : -1.33 (0.20), residues: 902 =============================================================================== Job complete usr+sys time: 2653.19 seconds wall clock time: 49 minutes 41.87 seconds (2981.87 seconds total)