Starting phenix.real_space_refine on Sun Mar 17 20:29:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tts_26122/03_2024/7tts_26122_updated.pdb" } resolution = 2.9 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= 0.006 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 4 5.21 5 S 54 5.16 5 C 11438 2.51 5 N 3615 2.21 5 O 3668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 327": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B ARG 417": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 561": "NH1" <-> "NH2" Residue "B ARG 590": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 629": "NH1" <-> "NH2" Residue "B ARG 650": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 342": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 417": "NH1" <-> "NH2" Residue "C ARG 475": "NH1" <-> "NH2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C ARG 561": "NH1" <-> "NH2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 629": "NH1" <-> "NH2" Residue "C ARG 650": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 408": "NH1" <-> "NH2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 475": "NH1" <-> "NH2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ARG 561": "NH1" <-> "NH2" Residue "D ARG 590": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D ARG 620": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 629": "NH1" <-> "NH2" Residue "D ARG 650": "NH1" <-> "NH2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E ARG 336": "NH1" <-> "NH2" Residue "E ARG 342": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E ARG 475": "NH1" <-> "NH2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E ARG 546": "NH1" <-> "NH2" Residue "E ARG 554": "NH1" <-> "NH2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "E ARG 561": "NH1" <-> "NH2" Residue "E ARG 590": "NH1" <-> "NH2" Residue "E ARG 594": "NH1" <-> "NH2" Residue "E ARG 603": "NH1" <-> "NH2" Residue "E ARG 620": "NH1" <-> "NH2" Residue "E ARG 628": "NH1" <-> "NH2" Residue "E ARG 629": "NH1" <-> "NH2" Residue "E ARG 650": "NH1" <-> "NH2" Residue "F ARG 327": "NH1" <-> "NH2" Residue "F ARG 329": "NH1" <-> "NH2" Residue "F ARG 334": "NH1" <-> "NH2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F ARG 336": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F ARG 362": "NH1" <-> "NH2" Residue "F ARG 363": "NH1" <-> "NH2" Residue "F ARG 408": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ARG 475": "NH1" <-> "NH2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "F ARG 561": "NH1" <-> "NH2" Residue "F ARG 590": "NH1" <-> "NH2" Residue "F ARG 594": "NH1" <-> "NH2" Residue "F ARG 603": "NH1" <-> "NH2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F ARG 628": "NH1" <-> "NH2" Residue "F ARG 629": "NH1" <-> "NH2" Residue "F ARG 650": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18793 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2980 Classifications: {'peptide': 433} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "B" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3033 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 12, 'TRANS': 427} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "C" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3159 Classifications: {'peptide': 456} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 15, 'TRANS': 440} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "D" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3217 Classifications: {'peptide': 463} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 16, 'TRANS': 446} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "E" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3199 Classifications: {'peptide': 461} Incomplete info: {'backbone_only': 120} Link IDs: {'PTRANS': 15, 'TRANS': 445} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "F" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 2980 Classifications: {'peptide': 433} Incomplete info: {'backbone_only': 120} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 420} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 7, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 231 Chain: "P" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.15, per 1000 atoms: 0.54 Number of scatterers: 18793 At special positions: 0 Unit cell: (133.6, 146.125, 140.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 14 15.00 Mg 4 11.99 O 3668 8.00 N 3615 7.00 C 11438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 4.3 seconds 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 15 sheets defined 52.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 269 through 275 Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 302 through 305 No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 310 through 335 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.946A pdb=" N ILE A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.208A pdb=" N GLN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 461 through 473 Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.683A pdb=" N HIS A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.664A pdb=" N GLY A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.569A pdb=" N ARG A 629 " --> pdb=" O GLU A 625 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 632 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLN A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 269 through 275 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 310 through 336 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.898A pdb=" N HIS B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 417 through 424 removed outlier: 3.694A pdb=" N ILE B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.586A pdb=" N THR B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 3.709A pdb=" N GLN B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 removed outlier: 3.886A pdb=" N ARG B 546 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 556 through 561 Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 603 through 612 removed outlier: 3.784A pdb=" N GLY B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 629 Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 180 through 188 Processing helix chain 'C' and resid 269 through 275 Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 302 through 305 No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 310 through 336 Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.528A pdb=" N GLU C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 417 through 424 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.844A pdb=" N THR C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET C 467 " --> pdb=" O VAL C 463 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLN C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.983A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLN C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 552 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.987A pdb=" N ARG C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 595 Processing helix chain 'C' and resid 603 through 612 removed outlier: 3.736A pdb=" N ASP C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP C 611 " --> pdb=" O ASP C 607 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY C 612 " --> pdb=" O VAL C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 640 removed outlier: 4.787A pdb=" N VAL C 631 " --> pdb=" O ARG C 628 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN C 632 " --> pdb=" O ARG C 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 639 " --> pdb=" O ALA C 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 302 through 305 No H-bonds generated for 'chain 'D' and resid 302 through 305' Processing helix chain 'D' and resid 310 through 335 Processing helix chain 'D' and resid 339 through 346 removed outlier: 3.642A pdb=" N HIS D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 365 Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'D' and resid 417 through 424 Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 461 through 473 removed outlier: 4.003A pdb=" N ILE D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET D 467 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D 468 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 470 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 515 removed outlier: 3.726A pdb=" N GLU D 515 " --> pdb=" O GLN D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 543 No H-bonds generated for 'chain 'D' and resid 540 through 543' Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.554A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.923A pdb=" N GLY D 612 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 629 removed outlier: 3.625A pdb=" N ARG D 629 " --> pdb=" O VAL D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 637 Processing helix chain 'E' and resid 133 through 144 Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 269 through 275 Processing helix chain 'E' and resid 279 through 288 Processing helix chain 'E' and resid 302 through 305 No H-bonds generated for 'chain 'E' and resid 302 through 305' Processing helix chain 'E' and resid 310 through 334 removed outlier: 4.256A pdb=" N GLN E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG E 327 " --> pdb=" O GLN E 323 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 346 removed outlier: 3.543A pdb=" N GLU E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 366 Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 411 through 413 No H-bonds generated for 'chain 'E' and resid 411 through 413' Processing helix chain 'E' and resid 417 through 424 removed outlier: 3.538A pdb=" N VAL E 420 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'E' and resid 499 through 516 Processing helix chain 'E' and resid 539 through 553 Proline residue: E 547 - end of helix Processing helix chain 'E' and resid 556 through 561 Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 603 through 612 removed outlier: 3.873A pdb=" N GLY E 612 " --> pdb=" O VAL E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 629 removed outlier: 3.625A pdb=" N ARG E 629 " --> pdb=" O VAL E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 638 Processing helix chain 'F' and resid 133 through 143 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 170 through 176 Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 269 through 276 Processing helix chain 'F' and resid 279 through 287 Processing helix chain 'F' and resid 302 through 305 No H-bonds generated for 'chain 'F' and resid 302 through 305' Processing helix chain 'F' and resid 310 through 336 Processing helix chain 'F' and resid 339 through 346 removed outlier: 4.034A pdb=" N HIS F 346 " --> pdb=" O ARG F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 Processing helix chain 'F' and resid 387 through 398 Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'F' and resid 419 through 422 No H-bonds generated for 'chain 'F' and resid 419 through 422' Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 461 through 470 removed outlier: 3.642A pdb=" N LEU F 468 " --> pdb=" O LEU F 464 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN F 469 " --> pdb=" O THR F 465 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU F 470 " --> pdb=" O ILE F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 503 Processing helix chain 'F' and resid 507 through 510 No H-bonds generated for 'chain 'F' and resid 507 through 510' Processing helix chain 'F' and resid 549 through 553 Processing helix chain 'F' and resid 573 through 590 Processing helix chain 'F' and resid 594 through 596 No H-bonds generated for 'chain 'F' and resid 594 through 596' Processing helix chain 'F' and resid 602 through 611 removed outlier: 3.635A pdb=" N ASP F 611 " --> pdb=" O ASP F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 629 Processing helix chain 'F' and resid 631 through 639 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 568 removed outlier: 4.051A pdb=" N GLY A 381 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= C, first strand: chain 'B' and resid 564 through 568 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= E, first strand: chain 'B' and resid 598 through 601 Processing sheet with id= F, first strand: chain 'C' and resid 564 through 568 removed outlier: 3.667A pdb=" N GLY C 381 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 475 through 477 Processing sheet with id= H, first strand: chain 'C' and resid 598 through 601 Processing sheet with id= I, first strand: chain 'D' and resid 564 through 568 Processing sheet with id= J, first strand: chain 'D' and resid 598 through 600 Processing sheet with id= K, first strand: chain 'E' and resid 564 through 568 Processing sheet with id= L, first strand: chain 'E' and resid 475 through 477 Processing sheet with id= M, first strand: chain 'E' and resid 597 through 600 removed outlier: 5.722A pdb=" N GLY E 645 " --> pdb=" O THR E 598 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU E 600 " --> pdb=" O GLY E 645 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS E 647 " --> pdb=" O LEU E 600 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR E 648 " --> pdb=" O GLN E 659 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 564 through 567 Processing sheet with id= O, first strand: chain 'F' and resid 474 through 477 removed outlier: 4.524A pdb=" N ILE F 484 " --> pdb=" O ARG F 475 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2604 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: 6.88 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6709 1.34 - 1.48: 4537 1.48 - 1.63: 7741 1.63 - 1.78: 18 1.78 - 1.93: 79 Bond restraints: 19084 Sorted by residual: bond pdb=" O2B AGS B 802 " pdb=" PB AGS B 802 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.60e-02 3.91e+03 3.33e+02 bond pdb=" O2A AGS B 802 " pdb=" PA AGS B 802 " ideal model delta sigma weight residual 1.531 1.264 0.267 1.60e-02 3.91e+03 2.79e+02 bond pdb=" C8 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.370 1.190 0.180 1.10e-02 8.26e+03 2.69e+02 bond pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " ideal model delta sigma weight residual 1.374 1.224 0.150 1.00e-02 1.00e+04 2.25e+02 bond pdb=" C3' AGS B 802 " pdb=" C4' AGS B 802 " ideal model delta sigma weight residual 1.526 1.390 0.136 1.10e-02 8.26e+03 1.54e+02 ... (remaining 19079 not shown) Histogram of bond angle deviations from ideal: 91.26 - 102.60: 51 102.60 - 113.95: 10197 113.95 - 125.29: 14867 125.29 - 136.64: 283 136.64 - 147.99: 2 Bond angle restraints: 25400 Sorted by residual: angle pdb=" C4 AGS E 801 " pdb=" N9 AGS E 801 " pdb=" C8 AGS E 801 " ideal model delta sigma weight residual 105.70 115.48 -9.78 4.55e-01 4.83e+00 4.62e+02 angle pdb=" C4 AGS C 802 " pdb=" N9 AGS C 802 " pdb=" C8 AGS C 802 " ideal model delta sigma weight residual 105.70 115.39 -9.69 4.55e-01 4.83e+00 4.53e+02 angle pdb=" C4 AGS B 802 " pdb=" N9 AGS B 802 " pdb=" C8 AGS B 802 " ideal model delta sigma weight residual 105.70 113.17 -7.47 4.55e-01 4.83e+00 2.70e+02 angle pdb=" N1 AGS B 802 " pdb=" C2 AGS B 802 " pdb=" N3 AGS B 802 " ideal model delta sigma weight residual 128.80 118.57 10.23 8.41e-01 1.41e+00 1.48e+02 angle pdb=" N7 AGS E 801 " pdb=" C8 AGS E 801 " pdb=" N9 AGS E 801 " ideal model delta sigma weight residual 114.03 105.71 8.32 6.99e-01 2.05e+00 1.42e+02 ... (remaining 25395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.51: 10135 25.51 - 51.02: 318 51.02 - 76.54: 58 76.54 - 102.05: 7 102.05 - 127.56: 4 Dihedral angle restraints: 10522 sinusoidal: 4187 harmonic: 6335 Sorted by residual: dihedral pdb=" C4' ADP A 801 " pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -180.00 -52.79 -127.21 1 2.00e+01 2.50e-03 3.85e+01 dihedral pdb=" C2' ADP A 801 " pdb=" C1' ADP A 801 " pdb=" N9 ADP A 801 " pdb=" C4 ADP A 801 " ideal model delta sinusoidal sigma weight residual 91.55 -143.32 -125.13 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" C VAL B 653 " pdb=" N VAL B 653 " pdb=" CA VAL B 653 " pdb=" CB VAL B 653 " ideal model delta harmonic sigma weight residual -122.00 -134.99 12.99 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 10519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2334 0.384 - 0.768: 3 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.920: 2 Chirality restraints: 2339 Sorted by residual: chirality pdb=" PB AGS B 802 " pdb=" O2B AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O3B AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.26 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" PA AGS B 802 " pdb=" O2A AGS B 802 " pdb=" O3A AGS B 802 " pdb=" O5' AGS B 802 " both_signs ideal model delta sigma weight residual True 3.18 -1.56 1.62 2.00e-01 2.50e+01 6.55e+01 chirality pdb=" C2' AGS B 802 " pdb=" C1' AGS B 802 " pdb=" C3' AGS B 802 " pdb=" O2' AGS B 802 " both_signs ideal model delta sigma weight residual False -2.67 -2.02 -0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 2336 not shown) Planarity restraints: 3555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 423 " -0.102 2.00e-02 2.50e+03 6.39e-02 7.14e+01 pdb=" CG PHE B 423 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE B 423 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE B 423 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE B 423 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 423 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 423 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS D 801 " -0.088 2.00e-02 2.50e+03 4.45e-02 5.44e+01 pdb=" C2 AGS D 801 " 0.041 2.00e-02 2.50e+03 pdb=" C4 AGS D 801 " -0.018 2.00e-02 2.50e+03 pdb=" C5 AGS D 801 " -0.016 2.00e-02 2.50e+03 pdb=" C6 AGS D 801 " -0.006 2.00e-02 2.50e+03 pdb=" C8 AGS D 801 " 0.068 2.00e-02 2.50e+03 pdb=" N1 AGS D 801 " 0.020 2.00e-02 2.50e+03 pdb=" N3 AGS D 801 " -0.002 2.00e-02 2.50e+03 pdb=" N6 AGS D 801 " -0.062 2.00e-02 2.50e+03 pdb=" N7 AGS D 801 " 0.011 2.00e-02 2.50e+03 pdb=" N9 AGS D 801 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 601 " -0.084 2.00e-02 2.50e+03 4.55e-02 5.16e+01 pdb=" CG TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 601 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 601 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP B 601 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 601 " 0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 601 " -0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 601 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 601 " -0.059 2.00e-02 2.50e+03 ... (remaining 3552 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 80 2.41 - 3.03: 12990 3.03 - 3.66: 27981 3.66 - 4.28: 42046 4.28 - 4.90: 68605 Nonbonded interactions: 151702 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O2G AGS B 802 " model vdw 1.788 2.170 nonbonded pdb=" O1B AGS D 801 " pdb="MG MG D 802 " model vdw 1.905 2.170 nonbonded pdb=" O1A AGS D 801 " pdb="MG MG D 802 " model vdw 2.012 2.170 nonbonded pdb=" OE2 GLU D 455 " pdb="MG MG D 802 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR E 388 " pdb="MG MG E 802 " model vdw 2.161 2.170 ... (remaining 151697 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 132 through 653) selection = (chain 'B' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'C' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'D' and (resid 132 through 515 or resid 539 through 653)) selection = (chain 'E' and (resid 132 through 515 or resid 539 through 653)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 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: 0.020 Extract box with map and model: 9.730 Check model and map are aligned: 0.280 Set scattering table: 0.200 Process input model: 53.950 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.110 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 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 : 0.008 0.292 19084 Z= 0.568 Angle : 0.995 20.677 25400 Z= 0.678 Chirality : 0.079 1.920 2339 Planarity : 0.005 0.080 3555 Dihedral : 12.972 127.559 6910 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 0.30 % Allowed : 1.28 % Favored : 98.42 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % 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: 1.89 (0.17), residues: 2650 helix: 1.81 (0.14), residues: 1449 sheet: 0.59 (0.32), residues: 263 loop : 0.74 (0.23), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.004 TRP B 601 HIS 0.012 0.001 HIS B 418 PHE 0.102 0.005 PHE B 423 TYR 0.075 0.002 TYR A 430 ARG 0.009 0.000 ARG D 620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 1.0337 time to fit residues: 73.9152 Evaluate side-chains 53 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 40.0000 chunk 203 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 137 optimal weight: 100.0000 chunk 108 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN C 511 GLN C 595 HIS D 341 GLN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19084 Z= 0.169 Angle : 0.506 6.667 25400 Z= 0.267 Chirality : 0.039 0.157 2339 Planarity : 0.004 0.044 3555 Dihedral : 8.420 119.849 2955 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 0.30 % Allowed : 2.98 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.36 (0.17), residues: 2650 helix: 2.30 (0.14), residues: 1440 sheet: 0.20 (0.31), residues: 263 loop : 0.97 (0.23), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 601 HIS 0.016 0.001 HIS D 552 PHE 0.014 0.001 PHE C 540 TYR 0.008 0.001 TYR A 430 ARG 0.005 0.000 ARG D 546 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: F 411 MET cc_start: -0.1958 (mpm) cc_final: -0.3002 (mpp) outliers start: 5 outliers final: 0 residues processed: 56 average time/residue: 0.9280 time to fit residues: 63.4981 Evaluate side-chains 52 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.0370 chunk 75 optimal weight: 20.0000 chunk 202 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 263 optimal weight: 30.0000 chunk 217 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 195 optimal weight: 30.0000 overall best weight: 4.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 HIS ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19084 Z= 0.145 Angle : 0.452 6.594 25400 Z= 0.239 Chirality : 0.038 0.166 2339 Planarity : 0.003 0.043 3555 Dihedral : 8.182 118.901 2954 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 0.36 % Allowed : 4.13 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.40 (0.17), residues: 2650 helix: 2.34 (0.14), residues: 1450 sheet: 0.09 (0.30), residues: 276 loop : 1.03 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 368 HIS 0.011 0.001 HIS D 552 PHE 0.023 0.001 PHE A 471 TYR 0.009 0.001 TYR B 430 ARG 0.009 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 2.417 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 0.9074 time to fit residues: 62.1482 Evaluate side-chains 53 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 26 optimal weight: 0.0170 chunk 116 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 244 optimal weight: 50.0000 chunk 259 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 231 optimal weight: 0.0000 chunk 69 optimal weight: 20.0000 overall best weight: 3.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 HIS ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19084 Z= 0.132 Angle : 0.436 6.479 25400 Z= 0.231 Chirality : 0.037 0.138 2339 Planarity : 0.003 0.042 3555 Dihedral : 8.131 119.914 2954 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.24 % Allowed : 4.68 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.37 (0.17), residues: 2650 helix: 2.35 (0.14), residues: 1449 sheet: 0.01 (0.30), residues: 277 loop : 0.99 (0.23), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 587 HIS 0.010 0.001 HIS A 399 PHE 0.015 0.001 PHE A 471 TYR 0.007 0.001 TYR B 430 ARG 0.003 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 2.254 Fit side-chains revert: symmetry clash REVERT: B 602 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6380 (p0) REVERT: F 411 MET cc_start: -0.1625 (mpm) cc_final: -0.2127 (mpp) outliers start: 4 outliers final: 0 residues processed: 56 average time/residue: 0.8664 time to fit residues: 60.4965 Evaluate side-chains 53 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 602 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 106 optimal weight: 40.0000 chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 chunk 0 optimal weight: 620.0000 chunk 132 optimal weight: 220.0000 chunk 232 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 GLN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5702 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19084 Z= 0.164 Angle : 0.457 6.488 25400 Z= 0.242 Chirality : 0.037 0.143 2339 Planarity : 0.003 0.038 3555 Dihedral : 8.159 120.898 2954 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 0.30 % Allowed : 5.35 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.34 (0.17), residues: 2650 helix: 2.32 (0.14), residues: 1459 sheet: -0.14 (0.29), residues: 277 loop : 0.99 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 368 HIS 0.009 0.001 HIS D 552 PHE 0.014 0.001 PHE A 471 TYR 0.009 0.001 TYR B 430 ARG 0.004 0.000 ARG D 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 2.331 Fit side-chains REVERT: F 411 MET cc_start: -0.1705 (mpm) cc_final: -0.2406 (mpp) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.9053 time to fit residues: 60.7897 Evaluate side-chains 54 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain E residue 401 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 220.0000 chunk 233 optimal weight: 4.9990 chunk 51 optimal weight: 50.0000 chunk 152 optimal weight: 0.0060 chunk 63 optimal weight: 0.0980 chunk 259 optimal weight: 9.9990 chunk 215 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 85 optimal weight: 0.0670 chunk 136 optimal weight: 6.9990 overall best weight: 2.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 ASN ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 19084 Z= 0.122 Angle : 0.441 7.858 25400 Z= 0.229 Chirality : 0.038 0.146 2339 Planarity : 0.003 0.037 3555 Dihedral : 8.106 121.580 2954 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.68 % Favored : 97.21 % Rotamer: Outliers : 0.24 % Allowed : 5.96 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.35 (0.17), residues: 2650 helix: 2.35 (0.14), residues: 1465 sheet: -0.12 (0.29), residues: 276 loop : 0.95 (0.23), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 587 HIS 0.009 0.001 HIS C 399 PHE 0.014 0.001 PHE A 471 TYR 0.006 0.001 TYR E 369 ARG 0.002 0.000 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 2.249 Fit side-chains REVERT: F 411 MET cc_start: -0.1712 (mpm) cc_final: -0.2296 (mpt) outliers start: 4 outliers final: 0 residues processed: 56 average time/residue: 0.9159 time to fit residues: 63.3090 Evaluate side-chains 52 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 7.9990 chunk 29 optimal weight: 50.0000 chunk 147 optimal weight: 50.0000 chunk 189 optimal weight: 30.0000 chunk 146 optimal weight: 20.0000 chunk 218 optimal weight: 0.0670 chunk 144 optimal weight: 50.0000 chunk 258 optimal weight: 8.9990 chunk 161 optimal weight: 40.0000 chunk 157 optimal weight: 6.9990 chunk 119 optimal weight: 0.0670 overall best weight: 4.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 595 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19084 Z= 0.145 Angle : 0.458 9.791 25400 Z= 0.239 Chirality : 0.038 0.190 2339 Planarity : 0.003 0.037 3555 Dihedral : 8.111 122.136 2954 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.98 % Rotamer: Outliers : 0.43 % Allowed : 5.84 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.37 (0.17), residues: 2650 helix: 2.35 (0.14), residues: 1470 sheet: -0.10 (0.29), residues: 276 loop : 0.97 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 368 HIS 0.012 0.001 HIS C 399 PHE 0.010 0.001 PHE A 471 TYR 0.007 0.001 TYR B 430 ARG 0.003 0.000 ARG D 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 411 MET cc_start: -0.1617 (mpm) cc_final: -0.2211 (mpt) outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.8735 time to fit residues: 61.6193 Evaluate side-chains 55 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 50 optimal weight: 50.0000 chunk 164 optimal weight: 9.9990 chunk 175 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 24 optimal weight: 40.0000 chunk 203 optimal weight: 20.0000 chunk 234 optimal weight: 0.0670 overall best weight: 7.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 581 ASN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19084 Z= 0.189 Angle : 0.511 10.563 25400 Z= 0.266 Chirality : 0.038 0.183 2339 Planarity : 0.003 0.036 3555 Dihedral : 8.212 123.898 2954 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 0.43 % Allowed : 6.14 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.33 (0.17), residues: 2650 helix: 2.31 (0.14), residues: 1470 sheet: -0.15 (0.30), residues: 268 loop : 0.97 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 368 HIS 0.009 0.001 HIS B 399 PHE 0.041 0.002 PHE A 453 TYR 0.009 0.001 TYR E 369 ARG 0.005 0.000 ARG D 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 2.109 Fit side-chains REVERT: F 411 MET cc_start: -0.1355 (mpm) cc_final: -0.1852 (mpt) outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.8871 time to fit residues: 63.3243 Evaluate side-chains 57 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain E residue 401 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 10.0000 chunk 225 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 189 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 overall best weight: 7.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 HIS ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19084 Z= 0.206 Angle : 0.546 9.860 25400 Z= 0.282 Chirality : 0.039 0.197 2339 Planarity : 0.003 0.035 3555 Dihedral : 8.320 128.862 2954 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.17 (0.17), residues: 2650 helix: 2.22 (0.14), residues: 1471 sheet: -0.32 (0.30), residues: 262 loop : 0.86 (0.23), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 368 HIS 0.015 0.001 HIS A 399 PHE 0.013 0.002 PHE E 453 TYR 0.014 0.001 TYR A 397 ARG 0.004 0.000 ARG D 590 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: E 467 MET cc_start: 0.8254 (pmm) cc_final: 0.8035 (pmm) REVERT: F 411 MET cc_start: -0.1144 (mpm) cc_final: -0.1635 (mpt) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.9129 time to fit residues: 61.8636 Evaluate side-chains 56 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 176 optimal weight: 50.0000 chunk 266 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 130 optimal weight: 50.0000 chunk 168 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19084 Z= 0.158 Angle : 0.518 11.881 25400 Z= 0.265 Chirality : 0.038 0.216 2339 Planarity : 0.003 0.039 3555 Dihedral : 8.315 133.426 2954 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 0.24 % Allowed : 6.26 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.17 (0.17), residues: 2650 helix: 2.25 (0.14), residues: 1469 sheet: -0.39 (0.30), residues: 262 loop : 0.84 (0.23), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 368 HIS 0.032 0.001 HIS A 399 PHE 0.017 0.001 PHE E 453 TYR 0.009 0.001 TYR E 369 ARG 0.003 0.000 ARG E 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 2.377 Fit side-chains revert: symmetry clash REVERT: E 467 MET cc_start: 0.8239 (pmm) cc_final: 0.8014 (pmm) REVERT: F 411 MET cc_start: -0.0827 (mpm) cc_final: -0.1375 (mpt) outliers start: 4 outliers final: 5 residues processed: 55 average time/residue: 0.9153 time to fit residues: 61.9997 Evaluate side-chains 57 residues out of total 2251 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain F residue 504 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 40.0000 chunk 65 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 89 optimal weight: 50.0000 chunk 218 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 186 optimal weight: 320.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 HIS ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.028794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.025831 restraints weight = 381754.026| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 6.09 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4419 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19084 Z= 0.177 Angle : 0.538 10.923 25400 Z= 0.275 Chirality : 0.038 0.204 2339 Planarity : 0.003 0.042 3555 Dihedral : 8.323 134.951 2954 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.43 % Favored : 96.49 % Rotamer: Outliers : 0.43 % Allowed : 6.08 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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: 2.16 (0.17), residues: 2650 helix: 2.24 (0.14), residues: 1468 sheet: -0.46 (0.30), residues: 261 loop : 0.83 (0.23), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 368 HIS 0.026 0.001 HIS A 399 PHE 0.022 0.001 PHE A 453 TYR 0.009 0.001 TYR E 369 ARG 0.004 0.000 ARG D 590 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.48 seconds wall clock time: 63 minutes 49.28 seconds (3829.28 seconds total)