Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 11 01:58:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xn7_22269/10_2023/6xn7_22269.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 73 5.49 5 S 52 5.16 5 C 13874 2.51 5 N 3771 2.21 5 O 4442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 623": "NH1" <-> "NH2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I GLU 120": "OE1" <-> "OE2" Residue "I GLU 136": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J GLU 21": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J GLU 206": "OE1" <-> "OE2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 304": "NH1" <-> "NH2" Residue "J ARG 311": "NH1" <-> "NH2" Residue "J GLU 341": "OE1" <-> "OE2" Residue "J ARG 346": "NH1" <-> "NH2" Residue "C GLU 13": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 137": "OE1" <-> "OE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 22212 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6033 Classifications: {'peptide': 746} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PTRANS': 9, 'TRANS': 733} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2239 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 277, 2237 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 277, 2237 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2284 Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1617 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 207} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1673 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2515 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 11, 'TRANS': 294} Chain breaks: 3 Chain: "R" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 6, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 18, 'rna3p': 18} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain: "D" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1089 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "E" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain breaks: 1 Chain: "T" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 793 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 17, 'rna3p_pyr': 12} Link IDs: {'rna2p': 8, 'rna3p': 28} Time building chain proxies: 12.13, per 1000 atoms: 0.55 Number of scatterers: 22212 At special positions: 0 Unit cell: (118.14, 140.694, 206.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 73 15.00 O 4442 8.00 N 3771 7.00 C 13874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 405 " distance=2.06 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 418 " distance=1.97 Simple disulfide: pdb=" SG CYS A 402 " - pdb=" SG CYS A 421 " distance=2.15 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 418 " distance=2.08 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 421 " distance=1.95 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 421 " distance=1.97 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: 8.52 Conformation dependent library (CDL) restraints added in 3.2 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 31 sheets defined 43.9% alpha, 13.5% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.576A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.825A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.795A pdb=" N CYS A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.900A pdb=" N SER A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.793A pdb=" N SER A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.362A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.732A pdb=" N TYR A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.733A pdb=" N VAL A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A 200 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 201 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 202 through 225 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.739A pdb=" N GLU A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.770A pdb=" N ASP A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 269 through 295 removed outlier: 3.764A pdb=" N LEU A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 339 removed outlier: 3.879A pdb=" N ASP A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 4.140A pdb=" N TYR A 368 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 418 through 431 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.772A pdb=" N LYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.712A pdb=" N ASN A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 485' Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 538 through 564 removed outlier: 3.923A pdb=" N SER A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASN A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.243A pdb=" N ILE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 637 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 668 through 681 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.781A pdb=" N LEU A 698 " --> pdb=" O ARG A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 3.842A pdb=" N ASN A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 removed outlier: 3.869A pdb=" N ILE A 724 " --> pdb=" O MET A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 739 Processing helix chain 'A' and resid 739 through 754 removed outlier: 3.554A pdb=" N LEU A 743 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 745 " --> pdb=" O LYS A 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.683A pdb=" N GLY B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.544A pdb=" N PHE B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.812A pdb=" N GLU B 171 " --> pdb=" O GLU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'F' and resid 45 through 62 removed outlier: 3.649A pdb=" N ASN F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 82 removed outlier: 3.869A pdb=" N LEU F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 157 through 173 Processing helix chain 'F' and resid 204 through 213 removed outlier: 4.017A pdb=" N LEU F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 63 removed outlier: 3.514A pdb=" N LEU H 49 " --> pdb=" O PRO H 45 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 removed outlier: 3.930A pdb=" N ASP H 73 " --> pdb=" O PRO H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 82 Processing helix chain 'H' and resid 103 through 110 removed outlier: 3.604A pdb=" N PHE H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 173 Processing helix chain 'H' and resid 180 through 184 Processing helix chain 'H' and resid 205 through 213 removed outlier: 3.682A pdb=" N ILE H 211 " --> pdb=" O THR H 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.878A pdb=" N ASP G 73 " --> pdb=" O PRO G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 103 through 110 removed outlier: 3.529A pdb=" N PHE G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 173 Processing helix chain 'G' and resid 205 through 212 Processing helix chain 'I' and resid 45 through 62 Processing helix chain 'I' and resid 69 through 73 removed outlier: 4.035A pdb=" N ASP I 73 " --> pdb=" O PRO I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 82 removed outlier: 4.789A pdb=" N LEU I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 Processing helix chain 'I' and resid 157 through 174 removed outlier: 3.584A pdb=" N PHE I 174 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 184 removed outlier: 3.509A pdb=" N ARG I 183 " --> pdb=" O HIS I 180 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY I 184 " --> pdb=" O GLY I 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 180 through 184' Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.541A pdb=" N ASN I 209 " --> pdb=" O ILE I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 50 removed outlier: 3.911A pdb=" N PHE J 45 " --> pdb=" O ASP J 41 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR J 46 " --> pdb=" O HIS J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 64 Processing helix chain 'J' and resid 70 through 74 removed outlier: 3.676A pdb=" N ASN J 74 " --> pdb=" O TYR J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 140 removed outlier: 3.711A pdb=" N LEU J 131 " --> pdb=" O PRO J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 226 Processing helix chain 'J' and resid 275 through 280 removed outlier: 3.612A pdb=" N LYS J 279 " --> pdb=" O GLY J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 303 removed outlier: 4.000A pdb=" N GLN J 301 " --> pdb=" O ASP J 297 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 302 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 38 Processing helix chain 'C' and resid 53 through 72 removed outlier: 4.276A pdb=" N VAL C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.595A pdb=" N GLU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 111 Processing helix chain 'C' and resid 112 through 123 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'D' and resid 25 through 38 removed outlier: 3.592A pdb=" N ILE D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 72 removed outlier: 3.727A pdb=" N LYS D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.550A pdb=" N GLU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'E' and resid 25 through 39 Processing helix chain 'E' and resid 55 through 73 removed outlier: 4.572A pdb=" N LYS E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.519A pdb=" N LEU E 84 " --> pdb=" O SER E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.543A pdb=" N LYS E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 125 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA2, first strand: chain 'A' and resid 304 through 305 removed outlier: 3.594A pdb=" N THR A 350 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 348 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.302A pdb=" N ILE A 473 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.678A pdb=" N SER A 607 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.678A pdb=" N SER A 607 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 651 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 65 removed outlier: 6.213A pdb=" N PHE B 59 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLU B 160 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 61 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU B 158 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 7 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 264 through 265 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 275 Processing sheet with id=AB3, first strand: chain 'F' and resid 94 through 95 removed outlier: 6.821A pdb=" N LYS F 2 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR F 8 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN F 192 " --> pdb=" O THR F 8 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 10 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE F 190 " --> pdb=" O VAL F 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 84 Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 120 Processing sheet with id=AB7, first strand: chain 'H' and resid 188 through 197 removed outlier: 5.500A pdb=" N PHE H 190 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL H 10 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN H 192 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR H 8 " --> pdb=" O ASN H 192 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE H 146 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU H 147 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN H 97 " --> pdb=" O GLU H 147 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY G 184 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE H 96 " --> pdb=" O GLY G 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'H' and resid 115 through 123 Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 95 removed outlier: 3.557A pdb=" N GLY G 7 " --> pdb=" O PHE G 146 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LYS G 2 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR G 197 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 4 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL G 195 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU G 6 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU G 193 " --> pdb=" O GLU G 6 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC3, first strand: chain 'G' and resid 115 through 120 Processing sheet with id=AC4, first strand: chain 'I' and resid 94 through 95 removed outlier: 3.726A pdb=" N PHE I 146 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR I 8 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN I 192 " --> pdb=" O THR I 8 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 10 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE I 190 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC6, first strand: chain 'I' and resid 115 through 120 Processing sheet with id=AC7, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.529A pdb=" N PHE J 203 " --> pdb=" O LYS J 3 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AC9, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.862A pdb=" N GLU J 189 " --> pdb=" O ASN J 114 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU J 184 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP J 176 " --> pdb=" O LEU J 184 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU J 186 " --> pdb=" O LYS J 174 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 174 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN J 173 " --> pdb=" O ASN J 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 29 through 31 removed outlier: 3.809A pdb=" N PHE J 30 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS J 38 " --> pdb=" O PHE J 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'D' and resid 13 through 15 902 hydrogen bonds defined for protein. 2589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 6817 1.34 - 1.47: 6051 1.47 - 1.61: 9770 1.61 - 1.75: 5 1.75 - 1.88: 97 Bond restraints: 22740 Sorted by residual: bond pdb=" C ASN H 68 " pdb=" N GLU H 69 " ideal model delta sigma weight residual 1.331 1.234 0.096 1.48e-02 4.57e+03 4.23e+01 bond pdb=" CG1 ILE G 77 " pdb=" CD1 ILE G 77 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.60e+00 bond pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " ideal model delta sigma weight residual 1.527 1.562 -0.035 1.30e-02 5.92e+03 7.23e+00 bond pdb=" CG1 ILE C 37 " pdb=" CD1 ILE C 37 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.36e+00 bond pdb=" CB CYS A 421 " pdb=" SG CYS A 421 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 5.02e+00 ... (remaining 22735 not shown) Histogram of bond angle deviations from ideal: 95.47 - 103.82: 394 103.82 - 112.17: 10930 112.17 - 120.52: 11274 120.52 - 128.88: 8224 128.88 - 137.23: 143 Bond angle restraints: 30965 Sorted by residual: angle pdb=" C SER H 20 " pdb=" N SER H 21 " pdb=" CA SER H 21 " ideal model delta sigma weight residual 121.70 137.23 -15.53 1.80e+00 3.09e-01 7.44e+01 angle pdb=" N GLY G 14 " pdb=" CA GLY G 14 " pdb=" C GLY G 14 " ideal model delta sigma weight residual 112.50 120.04 -7.54 1.16e+00 7.43e-01 4.23e+01 angle pdb=" C ASN G 62 " pdb=" N ASN G 63 " pdb=" CA ASN G 63 " ideal model delta sigma weight residual 121.70 133.27 -11.57 1.80e+00 3.09e-01 4.13e+01 angle pdb=" C ASN H 68 " pdb=" N GLU H 69 " pdb=" CA GLU H 69 " ideal model delta sigma weight residual 121.03 130.39 -9.36 1.60e+00 3.91e-01 3.42e+01 angle pdb=" C ASN D 44 " pdb=" N SER D 45 " pdb=" CA SER D 45 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.67e+01 ... (remaining 30960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 13197 33.69 - 67.39: 378 67.39 - 101.08: 24 101.08 - 134.78: 1 134.78 - 168.47: 3 Dihedral angle restraints: 13603 sinusoidal: 6106 harmonic: 7497 Sorted by residual: dihedral pdb=" CB CYS A 405 " pdb=" SG CYS A 405 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual -86.00 -173.73 87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 402 " pdb=" SG CYS A 402 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual 93.00 9.96 83.04 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" O4' U R 30 " pdb=" C1' U R 30 " pdb=" N1 U R 30 " pdb=" C2 U R 30 " ideal model delta sinusoidal sigma weight residual 200.00 34.65 165.35 1 1.50e+01 4.44e-03 8.39e+01 ... (remaining 13600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2998 0.083 - 0.165: 478 0.165 - 0.248: 42 0.248 - 0.331: 2 0.331 - 0.414: 5 Chirality restraints: 3525 Sorted by residual: chirality pdb=" CB ILE A 532 " pdb=" CA ILE A 532 " pdb=" CG1 ILE A 532 " pdb=" CG2 ILE A 532 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 509 " pdb=" CA VAL A 509 " pdb=" CG1 VAL A 509 " pdb=" CG2 VAL A 509 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CG LEU D 61 " pdb=" CB LEU D 61 " pdb=" CD1 LEU D 61 " pdb=" CD2 LEU D 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 3522 not shown) Planarity restraints: 3706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 111 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C ASN G 111 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN G 111 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL G 112 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 97 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" CD GLU E 97 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU E 97 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU E 97 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 69 " -0.052 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO H 70 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 70 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 70 " -0.043 5.00e-02 4.00e+02 ... (remaining 3703 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4350 2.77 - 3.30: 20424 3.30 - 3.83: 38078 3.83 - 4.37: 45383 4.37 - 4.90: 77808 Nonbonded interactions: 186043 Sorted by model distance: nonbonded pdb=" O SER I 24 " pdb=" OH TYR D 89 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR B 246 " pdb=" O LYS B 278 " model vdw 2.244 2.440 nonbonded pdb=" O TYR A 383 " pdb=" OH TYR B 232 " model vdw 2.258 2.440 nonbonded pdb=" OG SER I 47 " pdb=" OP1 G R 27 " model vdw 2.262 2.440 nonbonded pdb=" OG SER H 47 " pdb=" OP1 A R 21 " model vdw 2.267 2.440 ... (remaining 186038 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 'C' and (resid 16 through 43 or resid 50 through 146)) selection = (chain 'D' and (resid 16 through 43 or resid 50 through 146)) selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'H' and (resid 1 through 65 or resid 73 through 214)) selection = (chain 'I' and (resid 1 through 65 or resid 73 through 214)) } 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=0.50 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: 0.980 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: 4.920 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 60.410 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.007 0.119 22740 Z= 0.478 Angle : 1.101 15.526 30965 Z= 0.602 Chirality : 0.061 0.414 3525 Planarity : 0.006 0.078 3706 Dihedral : 15.517 168.471 8755 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.09 % Favored : 92.87 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.14), residues: 2540 helix: -1.97 (0.13), residues: 1047 sheet: -2.45 (0.23), residues: 385 loop : -2.44 (0.16), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 2.401 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 234 average time/residue: 0.3731 time to fit residues: 133.5901 Evaluate side-chains 169 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2116 time to fit residues: 3.9314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN B 172 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22740 Z= 0.170 Angle : 0.604 10.645 30965 Z= 0.324 Chirality : 0.043 0.471 3525 Planarity : 0.004 0.057 3706 Dihedral : 11.522 163.396 3675 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.89 % Allowed : 6.00 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.15), residues: 2540 helix: -0.52 (0.15), residues: 1064 sheet: -2.14 (0.23), residues: 414 loop : -2.30 (0.17), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 2.487 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.3516 time to fit residues: 113.6178 Evaluate side-chains 173 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 2.484 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2121 time to fit residues: 8.4933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 209 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 HIS I 121 ASN I 167 GLN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22740 Z= 0.334 Angle : 0.655 11.285 30965 Z= 0.346 Chirality : 0.046 0.507 3525 Planarity : 0.004 0.046 3706 Dihedral : 11.659 167.507 3675 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.03 % Allowed : 10.60 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.01 (0.16), residues: 2540 helix: -0.10 (0.16), residues: 1077 sheet: -2.06 (0.23), residues: 412 loop : -2.30 (0.17), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 189 average time/residue: 0.3589 time to fit residues: 106.1179 Evaluate side-chains 170 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 2.530 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2598 time to fit residues: 8.6841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 235 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22740 Z= 0.282 Angle : 0.610 11.130 30965 Z= 0.324 Chirality : 0.044 0.481 3525 Planarity : 0.004 0.046 3706 Dihedral : 11.526 163.305 3675 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.43 % Allowed : 12.53 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.76 (0.16), residues: 2540 helix: 0.20 (0.16), residues: 1080 sheet: -2.03 (0.23), residues: 415 loop : -2.23 (0.17), residues: 1045 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 187 average time/residue: 0.3478 time to fit residues: 102.7589 Evaluate side-chains 176 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2048 time to fit residues: 11.1806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 185 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22740 Z= 0.186 Angle : 0.552 10.689 30965 Z= 0.293 Chirality : 0.042 0.447 3525 Planarity : 0.003 0.047 3706 Dihedral : 11.291 160.351 3675 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.89 % Allowed : 14.36 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.44 (0.16), residues: 2540 helix: 0.52 (0.16), residues: 1079 sheet: -1.85 (0.23), residues: 412 loop : -2.14 (0.18), residues: 1049 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 2.571 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 190 average time/residue: 0.3358 time to fit residues: 102.0988 Evaluate side-chains 161 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.1967 time to fit residues: 6.6339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 chunk 207 optimal weight: 0.0000 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 707 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22740 Z= 0.142 Angle : 0.525 10.411 30965 Z= 0.278 Chirality : 0.041 0.432 3525 Planarity : 0.003 0.046 3706 Dihedral : 11.129 158.541 3675 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.07 % Allowed : 15.21 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.17 (0.16), residues: 2540 helix: 0.78 (0.16), residues: 1077 sheet: -1.66 (0.24), residues: 412 loop : -2.06 (0.18), residues: 1051 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 2.649 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 194 average time/residue: 0.3495 time to fit residues: 108.8563 Evaluate side-chains 180 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 2.498 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.2055 time to fit residues: 9.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 0.3980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22740 Z= 0.168 Angle : 0.542 10.372 30965 Z= 0.284 Chirality : 0.042 0.437 3525 Planarity : 0.003 0.044 3706 Dihedral : 11.114 160.597 3675 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.72 % Allowed : 16.06 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.08 (0.16), residues: 2540 helix: 0.85 (0.16), residues: 1079 sheet: -1.59 (0.24), residues: 411 loop : -2.02 (0.18), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 2.526 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 179 average time/residue: 0.3384 time to fit residues: 98.1420 Evaluate side-chains 165 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 155 time to evaluate : 2.898 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2055 time to fit residues: 7.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.3980 chunk 74 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 226 optimal weight: 3.9990 overall best weight: 1.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22740 Z= 0.172 Angle : 0.540 11.310 30965 Z= 0.283 Chirality : 0.042 0.435 3525 Planarity : 0.003 0.044 3706 Dihedral : 11.103 160.935 3675 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.54 % Allowed : 16.51 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.00 (0.17), residues: 2540 helix: 0.91 (0.16), residues: 1079 sheet: -1.65 (0.24), residues: 393 loop : -1.93 (0.18), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 171 average time/residue: 0.3415 time to fit residues: 93.8198 Evaluate side-chains 162 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.2076 time to fit residues: 6.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 181 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 219 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22740 Z= 0.167 Angle : 0.541 11.010 30965 Z= 0.282 Chirality : 0.041 0.434 3525 Planarity : 0.003 0.043 3706 Dihedral : 11.087 161.041 3675 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.36 % Allowed : 17.00 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2540 helix: 0.97 (0.16), residues: 1072 sheet: -1.59 (0.25), residues: 392 loop : -1.92 (0.18), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 2.615 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 173 average time/residue: 0.3592 time to fit residues: 99.4359 Evaluate side-chains 162 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2010 time to fit residues: 5.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN H 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22740 Z= 0.192 Angle : 0.555 11.555 30965 Z= 0.290 Chirality : 0.042 0.445 3525 Planarity : 0.003 0.044 3706 Dihedral : 11.138 162.188 3675 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.31 % Allowed : 17.18 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2540 helix: 0.95 (0.16), residues: 1073 sheet: -1.59 (0.25), residues: 392 loop : -1.94 (0.18), residues: 1075 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 2.473 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 165 average time/residue: 0.3966 time to fit residues: 107.3177 Evaluate side-chains 159 residues out of total 2253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2091 time to fit residues: 5.4533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** 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 = 0.3553 r_free = 0.3553 target = 0.103705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084656 restraints weight = 66558.099| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.06 r_work: 0.3083 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 22740 Z= 0.288 Angle : 0.619 11.817 30965 Z= 0.322 Chirality : 0.045 0.476 3525 Planarity : 0.004 0.044 3706 Dihedral : 11.357 165.424 3675 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.45 % Allowed : 17.05 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.40 % 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: -1.12 (0.16), residues: 2540 helix: 0.76 (0.16), residues: 1078 sheet: -1.61 (0.25), residues: 389 loop : -1.98 (0.18), residues: 1073 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3762.46 seconds wall clock time: 70 minutes 35.05 seconds (4235.05 seconds total)