Starting phenix.real_space_refine on Mon Mar 18 10:14:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wht_21675/03_2024/6wht_21675.pdb" } resolution = 4.39 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= 0.012 sd= 0.650 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 74 5.16 5 C 13142 2.51 5 N 3376 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D TYR 762": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 20532 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 5250 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1265 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 44, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 4960 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 13, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 20, 'GLU:plan': 31, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 619 Chain: "C" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 5250 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1265 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 3, 'HIS:plan': 8, 'PHE:plan': 9, 'GLU:plan': 44, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 726 Chain: "D" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 4960 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 22, 'TYR:plan': 13, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 20, 'GLU:plan': 31, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 619 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.96, per 1000 atoms: 0.53 Number of scatterers: 20532 At special positions: 0 Unit cell: (137, 152.07, 183.58, 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 74 16.00 O 3940 8.00 N 3376 7.00 C 13142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1003 " - " ASN A 224 " " NAG B 901 " - " ASN B 542 " " NAG C1003 " - " ASN C 224 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN A 389 " " NAG F 1 " - " ASN C 389 " Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 3.7 seconds 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 36 sheets defined 45.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.532A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.223A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.697A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 3.888A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.618A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.129A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.785A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.637A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.254A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.752A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 654 removed outlier: 4.672A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 742 No H-bonds generated for 'chain 'B' and resid 741 through 742' Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 772 through 785 Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 818 through 837 removed outlier: 3.705A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.531A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.224A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.696A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.889A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.619A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 861 " --> pdb=" O ALA C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 removed outlier: 4.128A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.784A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 341 removed outlier: 3.636A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 568 through 579 removed outlier: 4.253A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.751A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 654 removed outlier: 4.673A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 724 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 742 No H-bonds generated for 'chain 'D' and resid 741 through 742' Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 772 through 785 Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 818 through 837 removed outlier: 3.704A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.506A pdb=" N ILE A 240 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.161A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.295A pdb=" N LEU A 419 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 498 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA9, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 751 Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB6, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.524A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.582A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.507A pdb=" N ILE C 240 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.160A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.294A pdb=" N LEU C 419 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS C 498 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 431 through 434 Processing sheet with id=AC8, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AC9, first strand: chain 'C' and resid 555 through 557 Processing sheet with id=AD1, first strand: chain 'C' and resid 750 through 751 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AD5, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.523A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 765 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD8, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.581A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2790 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: 8.18 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6723 1.34 - 1.46: 4937 1.46 - 1.58: 9156 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 20922 Sorted by residual: bond pdb=" C ALA A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.12e-02 7.97e+03 7.99e+00 bond pdb=" C ALA C 536 " pdb=" N PRO C 537 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.12e-02 7.97e+03 7.84e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" N GLY A 558 " pdb=" CA GLY A 558 " ideal model delta sigma weight residual 1.458 1.443 0.015 9.20e-03 1.18e+04 2.75e+00 ... (remaining 20917 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.38: 533 106.38 - 113.29: 12360 113.29 - 120.21: 6996 120.21 - 127.13: 8770 127.13 - 134.04: 235 Bond angle restraints: 28894 Sorted by residual: angle pdb=" C SER D 526 " pdb=" N VAL D 527 " pdb=" CA VAL D 527 " ideal model delta sigma weight residual 122.59 119.55 3.04 7.20e-01 1.93e+00 1.78e+01 angle pdb=" C SER B 526 " pdb=" N VAL B 527 " pdb=" CA VAL B 527 " ideal model delta sigma weight residual 122.59 119.63 2.96 7.20e-01 1.93e+00 1.69e+01 angle pdb=" C SER A 464 " pdb=" CA SER A 464 " pdb=" CB SER A 464 " ideal model delta sigma weight residual 111.20 108.48 2.72 7.10e-01 1.98e+00 1.47e+01 angle pdb=" CA CYS D 321 " pdb=" CB CYS D 321 " pdb=" SG CYS D 321 " ideal model delta sigma weight residual 114.40 123.21 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA CYS B 321 " pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 28889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 11695 24.79 - 49.59: 443 49.59 - 74.38: 50 74.38 - 99.17: 18 99.17 - 123.96: 6 Dihedral angle restraints: 12212 sinusoidal: 3330 harmonic: 8882 Sorted by residual: dihedral pdb=" CA CYS B 321 " pdb=" C CYS B 321 " pdb=" N TYR B 322 " pdb=" CA TYR B 322 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.74e+01 dihedral pdb=" CA CYS D 321 " pdb=" C CYS D 321 " pdb=" N TYR D 322 " pdb=" CA TYR D 322 " ideal model delta harmonic sigma weight residual -180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA ARG B 439 " pdb=" C ARG B 439 " pdb=" N ILE B 440 " pdb=" CA ILE B 440 " ideal model delta harmonic sigma weight residual 180.00 131.15 48.85 0 5.00e+00 4.00e-02 9.54e+01 ... (remaining 12209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 3736 0.223 - 0.446: 2 0.446 - 0.669: 0 0.669 - 0.892: 0 0.892 - 1.114: 2 Chirality restraints: 3740 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.10e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" CB VAL C 756 " pdb=" CA VAL C 756 " pdb=" CG1 VAL C 756 " pdb=" CG2 VAL C 756 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3737 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 415 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 415 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 680 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.036 5.00e-02 4.00e+02 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 288 2.57 - 3.15: 21015 3.15 - 3.73: 32165 3.73 - 4.32: 40631 4.32 - 4.90: 60657 Nonbonded interactions: 154756 Sorted by model distance: nonbonded pdb=" OG1 THR C 446 " pdb=" O GLY C 449 " model vdw 1.983 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" O GLY A 449 " model vdw 1.983 2.440 nonbonded pdb=" OG SER B 170 " pdb=" O ILE B 227 " model vdw 2.004 2.440 nonbonded pdb=" OG SER D 170 " pdb=" O ILE D 227 " model vdw 2.005 2.440 nonbonded pdb=" OG SER D 34 " pdb=" O VAL D 65 " model vdw 2.047 2.440 ... (remaining 154751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' 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 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.840 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 56.250 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 0.006 0.053 20922 Z= 0.429 Angle : 0.852 10.387 28894 Z= 0.485 Chirality : 0.053 1.114 3740 Planarity : 0.006 0.073 3682 Dihedral : 14.471 123.962 6412 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 17.34 % Favored : 82.33 % Rotamer: Outliers : 0.63 % Allowed : 11.45 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -5.16 (0.12), residues: 3034 helix: -2.83 (0.12), residues: 1140 sheet: -3.98 (0.24), residues: 284 loop : -3.89 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 559 HIS 0.008 0.002 HIS C 134 PHE 0.016 0.002 PHE D 822 TYR 0.031 0.003 TYR D 167 ARG 0.003 0.001 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7179 (mp) cc_final: 0.6860 (mp) REVERT: A 806 MET cc_start: 0.6967 (mmm) cc_final: 0.6741 (tpp) REVERT: C 125 MET cc_start: 0.7313 (mmm) cc_final: 0.6899 (mmm) REVERT: D 782 GLN cc_start: 0.6559 (tp40) cc_final: 0.6119 (tp40) outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.2185 time to fit residues: 76.7874 Evaluate side-chains 159 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 156 optimal weight: 40.0000 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 0.0010 chunk 92 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 0.0670 overall best weight: 1.4130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 118 GLN B 159 ASN B 184 ASN B 486 HIS B 615 ASN B 616 ASN C 50 ASN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 184 ASN D 486 HIS D 616 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20922 Z= 0.199 Angle : 0.695 12.964 28894 Z= 0.364 Chirality : 0.046 0.272 3740 Planarity : 0.005 0.069 3682 Dihedral : 9.383 89.804 3312 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.05 % Favored : 89.68 % Rotamer: Outliers : 0.46 % Allowed : 7.35 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.43 (0.14), residues: 3034 helix: -0.97 (0.14), residues: 1226 sheet: -3.29 (0.23), residues: 330 loop : -3.25 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 166 HIS 0.003 0.001 HIS C 726 PHE 0.013 0.002 PHE D 241 TYR 0.022 0.002 TYR A 724 ARG 0.003 0.001 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 222 time to evaluate : 2.089 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: A 121 LEU cc_start: 0.6666 (mp) cc_final: 0.6343 (mp) REVERT: A 806 MET cc_start: 0.6809 (mmm) cc_final: 0.6577 (tpp) REVERT: B 462 ILE cc_start: 0.8120 (mt) cc_final: 0.7855 (mm) REVERT: C 125 MET cc_start: 0.7211 (mmm) cc_final: 0.6806 (mmm) REVERT: C 154 MET cc_start: 0.6414 (tpp) cc_final: 0.6178 (tpp) REVERT: D 462 ILE cc_start: 0.8018 (mt) cc_final: 0.7229 (mt) outliers start: 8 outliers final: 2 residues processed: 230 average time/residue: 0.2216 time to fit residues: 88.8663 Evaluate side-chains 171 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 189 optimal weight: 0.0000 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 20.0000 chunk 276 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20922 Z= 0.206 Angle : 0.668 12.795 28894 Z= 0.349 Chirality : 0.045 0.279 3740 Planarity : 0.005 0.061 3682 Dihedral : 8.831 86.561 3312 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.37 % Favored : 88.50 % Rotamer: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.68 (0.15), residues: 3034 helix: -0.19 (0.14), residues: 1236 sheet: -2.95 (0.24), residues: 328 loop : -2.99 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 166 HIS 0.003 0.001 HIS C 134 PHE 0.014 0.001 PHE D 182 TYR 0.018 0.002 TYR B 167 ARG 0.005 0.000 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.323 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: B 462 ILE cc_start: 0.8163 (mt) cc_final: 0.7878 (mm) REVERT: C 125 MET cc_start: 0.7146 (mmm) cc_final: 0.6872 (mmm) REVERT: D 462 ILE cc_start: 0.8053 (mt) cc_final: 0.7692 (mm) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2238 time to fit residues: 76.6695 Evaluate side-chains 159 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 6.9990 chunk 209 optimal weight: 0.0870 chunk 144 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 186 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 264 optimal weight: 0.0050 chunk 79 optimal weight: 10.0000 overall best weight: 2.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 392 HIS ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20922 Z= 0.196 Angle : 0.648 12.695 28894 Z= 0.336 Chirality : 0.044 0.268 3740 Planarity : 0.005 0.061 3682 Dihedral : 8.446 84.751 3312 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.35 % Favored : 89.52 % Rotamer: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.21 (0.15), residues: 3034 helix: 0.27 (0.15), residues: 1224 sheet: -2.73 (0.25), residues: 328 loop : -2.76 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 166 HIS 0.003 0.001 HIS C 134 PHE 0.046 0.001 PHE B 241 TYR 0.022 0.002 TYR A 724 ARG 0.002 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 ILE cc_start: 0.8093 (mt) cc_final: 0.7857 (mm) REVERT: C 125 MET cc_start: 0.7211 (mmm) cc_final: 0.6984 (mmm) REVERT: D 462 ILE cc_start: 0.7959 (mt) cc_final: 0.7674 (mm) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2324 time to fit residues: 78.5211 Evaluate side-chains 159 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 147 GLN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS C 801 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20922 Z= 0.301 Angle : 0.709 13.482 28894 Z= 0.370 Chirality : 0.045 0.253 3740 Planarity : 0.005 0.059 3682 Dihedral : 8.549 86.899 3312 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.16 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.26 (0.15), residues: 3034 helix: 0.27 (0.15), residues: 1226 sheet: -2.79 (0.25), residues: 328 loop : -2.82 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 268 HIS 0.008 0.002 HIS A 134 PHE 0.042 0.002 PHE B 241 TYR 0.024 0.002 TYR B 167 ARG 0.001 0.000 ARG C 715 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.228 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: B 462 ILE cc_start: 0.8124 (mt) cc_final: 0.7914 (mm) REVERT: D 462 ILE cc_start: 0.8036 (mt) cc_final: 0.7762 (mm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2255 time to fit residues: 74.3811 Evaluate side-chains 156 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.0670 chunk 266 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20922 Z= 0.165 Angle : 0.638 12.610 28894 Z= 0.326 Chirality : 0.044 0.269 3740 Planarity : 0.005 0.066 3682 Dihedral : 7.916 81.154 3312 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.16 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.82 (0.16), residues: 3034 helix: 0.66 (0.15), residues: 1224 sheet: -2.36 (0.28), residues: 304 loop : -2.66 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 166 HIS 0.007 0.001 HIS C 134 PHE 0.010 0.001 PHE B 822 TYR 0.018 0.001 TYR C 724 ARG 0.001 0.000 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.104 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: B 462 ILE cc_start: 0.8170 (mt) cc_final: 0.7925 (mm) REVERT: D 462 ILE cc_start: 0.7842 (mt) cc_final: 0.7599 (mm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2316 time to fit residues: 77.1934 Evaluate side-chains 165 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 168 optimal weight: 0.0010 chunk 216 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 294 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 overall best weight: 4.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS D 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20922 Z= 0.248 Angle : 0.670 13.170 28894 Z= 0.347 Chirality : 0.045 0.364 3740 Planarity : 0.005 0.057 3682 Dihedral : 7.866 80.206 3312 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.40 % Favored : 88.56 % Rotamer: Outliers : 0.06 % Allowed : 1.65 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.84 (0.16), residues: 3034 helix: 0.65 (0.15), residues: 1224 sheet: -2.50 (0.26), residues: 324 loop : -2.63 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 268 HIS 0.004 0.001 HIS B 127 PHE 0.015 0.001 PHE D 822 TYR 0.024 0.002 TYR B 167 ARG 0.003 0.001 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7081 (ptp) cc_final: 0.6682 (ptp) REVERT: B 462 ILE cc_start: 0.8002 (mt) cc_final: 0.7779 (mm) REVERT: D 462 ILE cc_start: 0.7938 (mt) cc_final: 0.7684 (mm) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.2210 time to fit residues: 71.0955 Evaluate side-chains 155 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 176 optimal weight: 0.0020 chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 268 optimal weight: 0.0370 overall best weight: 1.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20922 Z= 0.156 Angle : 0.628 13.266 28894 Z= 0.318 Chirality : 0.044 0.261 3740 Planarity : 0.005 0.065 3682 Dihedral : 7.280 73.517 3312 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.50 % Favored : 91.46 % Rotamer: Outliers : 0.06 % Allowed : 1.14 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.56 (0.16), residues: 3034 helix: 0.85 (0.15), residues: 1246 sheet: -2.10 (0.28), residues: 304 loop : -2.57 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 166 HIS 0.003 0.001 HIS A 94 PHE 0.016 0.001 PHE B 182 TYR 0.021 0.001 TYR C 724 ARG 0.003 0.000 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7068 (ptp) cc_final: 0.6621 (ptp) REVERT: B 216 ILE cc_start: 0.6601 (pt) cc_final: 0.5934 (pt) REVERT: B 462 ILE cc_start: 0.8060 (mt) cc_final: 0.7817 (mm) REVERT: D 462 ILE cc_start: 0.7947 (mt) cc_final: 0.7690 (mm) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.2259 time to fit residues: 77.8666 Evaluate side-chains 163 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 274 optimal weight: 30.0000 chunk 165 optimal weight: 8.9990 chunk 119 optimal weight: 0.0030 chunk 215 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 259 optimal weight: 0.4980 chunk 273 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20922 Z= 0.210 Angle : 0.642 13.470 28894 Z= 0.329 Chirality : 0.044 0.388 3740 Planarity : 0.005 0.057 3682 Dihedral : 7.184 70.259 3312 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.55 % Favored : 89.42 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.54 (0.16), residues: 3034 helix: 0.85 (0.15), residues: 1234 sheet: -2.30 (0.27), residues: 324 loop : -2.45 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 268 HIS 0.003 0.001 HIS A 498 PHE 0.023 0.001 PHE B 182 TYR 0.020 0.002 TYR C 724 ARG 0.002 0.000 ARG A 743 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7167 (ptp) cc_final: 0.6734 (ptp) REVERT: B 462 ILE cc_start: 0.8059 (mt) cc_final: 0.7823 (mm) REVERT: D 462 ILE cc_start: 0.7871 (mt) cc_final: 0.7256 (mt) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2101 time to fit residues: 69.4778 Evaluate side-chains 157 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 20.0000 chunk 177 optimal weight: 0.0270 chunk 137 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 304 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 242 optimal weight: 0.0010 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN D 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20922 Z= 0.173 Angle : 0.628 13.082 28894 Z= 0.317 Chirality : 0.044 0.312 3740 Planarity : 0.004 0.063 3682 Dihedral : 6.835 62.164 3312 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.97 % Favored : 91.00 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.45 (0.16), residues: 3034 helix: 0.90 (0.15), residues: 1248 sheet: -2.01 (0.28), residues: 302 loop : -2.49 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 166 HIS 0.003 0.001 HIS C 94 PHE 0.023 0.001 PHE B 182 TYR 0.021 0.001 TYR C 724 ARG 0.003 0.000 ARG C 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 462 ILE cc_start: 0.7980 (mt) cc_final: 0.7756 (mm) REVERT: D 462 ILE cc_start: 0.8112 (mt) cc_final: 0.7526 (mt) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2161 time to fit residues: 71.0603 Evaluate side-chains 160 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.063270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052435 restraints weight = 161218.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053488 restraints weight = 107840.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054215 restraints weight = 80438.166| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20922 Z= 0.222 Angle : 0.647 13.314 28894 Z= 0.330 Chirality : 0.044 0.310 3740 Planarity : 0.005 0.058 3682 Dihedral : 6.706 54.584 3312 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.84 % Favored : 89.12 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.46 (0.16), residues: 3034 helix: 0.91 (0.15), residues: 1238 sheet: -2.34 (0.26), residues: 336 loop : -2.38 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 268 HIS 0.004 0.001 HIS C 94 PHE 0.023 0.001 PHE B 182 TYR 0.020 0.002 TYR D 167 ARG 0.002 0.000 ARG A 743 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.84 seconds wall clock time: 57 minutes 12.26 seconds (3432.26 seconds total)