Starting phenix.real_space_refine on Sun Dec 10 12:13:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns3_12559/12_2023/7ns3_12559.pdb" } resolution = 3.5 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19 atoms to isotropic. 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 68 5.16 5 C 9386 2.51 5 N 2403 2.21 5 O 2588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 56": "OD1" <-> "OD2" Residue "5 ASP 78": "OD1" <-> "OD2" Residue "5 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 122": "OD1" <-> "OD2" Residue "5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 194": "OE1" <-> "OE2" Residue "5 PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 299": "OD1" <-> "OD2" Residue "5 TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 348": "OD1" <-> "OD2" Residue "5 ASP 354": "OD1" <-> "OD2" Residue "5 ARG 386": "NH1" <-> "NH2" Residue "5 TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 473": "OD1" <-> "OD2" Residue "5 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 532": "OE1" <-> "OE2" Residue "5 PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 638": "OD1" <-> "OD2" Residue "5 PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 706": "OD1" <-> "OD2" Residue "5 ASP 754": "OD1" <-> "OD2" Residue "5 ARG 893": "NH1" <-> "NH2" Residue "5 ASP 898": "OD1" <-> "OD2" Residue "5 GLU 905": "OE1" <-> "OE2" Residue "5 ASP 915": "OD1" <-> "OD2" Residue "8 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 104": "OD1" <-> "OD2" Residue "8 ARG 108": "NH1" <-> "NH2" Residue "8 GLU 112": "OE1" <-> "OE2" Residue "8 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 133": "OE1" <-> "OE2" Residue "8 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 151": "OE1" <-> "OE2" Residue "8 GLU 152": "OE1" <-> "OE2" Residue "8 ASP 192": "OD1" <-> "OD2" Residue "8 ASP 221": "OD1" <-> "OD2" Residue "8 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 283": "NH1" <-> "NH2" Residue "8 ASP 288": "OD1" <-> "OD2" Residue "8 ARG 301": "NH1" <-> "NH2" Residue "8 PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 315": "OD1" <-> "OD2" Residue "8 PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 350": "OD1" <-> "OD2" Residue "8 ARG 374": "NH1" <-> "NH2" Residue "8 PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 426": "OE1" <-> "OE2" Residue "8 ARG 452": "NH1" <-> "NH2" Residue "1 ASP 9": "OD1" <-> "OD2" Residue "1 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 38": "NH1" <-> "NH2" Residue "1 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 110": "OD1" <-> "OD2" Residue "1 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 114": "NH1" <-> "NH2" Residue "1 PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 396": "OD1" <-> "OD2" Residue "1 PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 405": "OE1" <-> "OE2" Residue "1 PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 506": "OD1" <-> "OD2" Residue "1 PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 535": "NH1" <-> "NH2" Residue "1 PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 596": "OD1" <-> "OD2" Residue "1 GLU 610": "OE1" <-> "OE2" Residue "1 ARG 694": "NH1" <-> "NH2" Residue "1 ASP 741": "OD1" <-> "OD2" Residue "1 GLU 766": "OE1" <-> "OE2" Residue "1 ARG 777": "NH1" <-> "NH2" Residue "1 GLU 931": "OE1" <-> "OE2" Residue "1 PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 942": "OD1" <-> "OD2" Residue "1 ARG 944": "NH1" <-> "NH2" Residue "1 ASP 954": "OD1" <-> "OD2" Residue "9 GLU 226": "OE1" <-> "OE2" Residue "9 ARG 230": "NH1" <-> "NH2" Residue "9 PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 264": "OD1" <-> "OD2" Residue "9 PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 319": "NH1" <-> "NH2" Residue "9 ARG 346": "NH1" <-> "NH2" Residue "9 ASP 353": "OD1" <-> "OD2" Residue "4 TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 124": "NH1" <-> "NH2" Residue "4 ARG 126": "NH1" <-> "NH2" Residue "4 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 170": "NH1" <-> "NH2" Residue "4 TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 202": "OD1" <-> "OD2" Residue "4 GLU 203": "OE1" <-> "OE2" Residue "4 GLU 208": "OE1" <-> "OE2" Residue "4 ASP 213": "OD1" <-> "OD2" Residue "4 ARG 227": "NH1" <-> "NH2" Residue "4 PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 280": "OD1" <-> "OD2" Residue "4 TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 14445 Number of models: 1 Model: "" Number of chains: 6 Chain: "5" Number of atoms: 5919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5919 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 23, 'TRANS': 738} Chain breaks: 4 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 26, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 196 Chain: "8" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2597 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 2, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "1" Number of atoms: 3272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3272 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 14, 'TRANS': 409} Chain breaks: 8 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 115 Chain: "9" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1065 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain breaks: 3 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "4" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1570 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain breaks: 3 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "Fb" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Time building chain proxies: 7.84, per 1000 atoms: 0.54 Number of scatterers: 14445 At special positions: 0 Unit cell: (118.5, 121.66, 145.36, 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 68 16.00 O 2588 8.00 N 2403 7.00 C 9386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 656 " - pdb=" SG CYS 4 357 " 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 Time building additional restraints: 5.84 Conformation dependent library (CDL) restraints added in 2.6 seconds 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 5 sheets defined 53.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain '5' and resid 7 through 16 Processing helix chain '5' and resid 21 through 28 removed outlier: 3.805A pdb=" N PHE 5 28 " --> pdb=" O LYS 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 39 removed outlier: 4.197A pdb=" N GLN 5 37 " --> pdb=" O CYS 5 33 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS 5 38 " --> pdb=" O GLN 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 49 through 61 Processing helix chain '5' and resid 66 through 72 Processing helix chain '5' and resid 74 through 85 Processing helix chain '5' and resid 92 through 96 Processing helix chain '5' and resid 98 through 114 Processing helix chain '5' and resid 123 through 137 Processing helix chain '5' and resid 145 through 160 removed outlier: 3.753A pdb=" N LEU 5 160 " --> pdb=" O LYS 5 156 " (cutoff:3.500A) Processing helix chain '5' and resid 188 through 206 removed outlier: 5.107A pdb=" N LYS 5 206 " --> pdb=" O LYS 5 202 " (cutoff:3.500A) Processing helix chain '5' and resid 255 through 271 Processing helix chain '5' and resid 285 through 296 removed outlier: 4.310A pdb=" N LYS 5 296 " --> pdb=" O LEU 5 292 " (cutoff:3.500A) Processing helix chain '5' and resid 300 through 316 Proline residue: 5 313 - end of helix Processing helix chain '5' and resid 324 through 338 Proline residue: 5 332 - end of helix removed outlier: 4.176A pdb=" N PHE 5 338 " --> pdb=" O LEU 5 334 " (cutoff:3.500A) Processing helix chain '5' and resid 349 through 363 Processing helix chain '5' and resid 369 through 377 removed outlier: 3.854A pdb=" N THR 5 377 " --> pdb=" O THR 5 373 " (cutoff:3.500A) Processing helix chain '5' and resid 379 through 391 Processing helix chain '5' and resid 398 through 414 Processing helix chain '5' and resid 419 through 428 removed outlier: 4.608A pdb=" N ASP 5 428 " --> pdb=" O LEU 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 431 through 451 Processing helix chain '5' and resid 453 through 459 Processing helix chain '5' and resid 474 through 489 removed outlier: 4.016A pdb=" N ARG 5 489 " --> pdb=" O LYS 5 485 " (cutoff:3.500A) Processing helix chain '5' and resid 491 through 496 Processing helix chain '5' and resid 501 through 520 Processing helix chain '5' and resid 526 through 546 Proline residue: 5 531 - end of helix removed outlier: 3.526A pdb=" N GLY 5 541 " --> pdb=" O GLY 5 537 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN 5 545 " --> pdb=" O GLY 5 541 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE 5 546 " --> pdb=" O SER 5 542 " (cutoff:3.500A) Processing helix chain '5' and resid 553 through 560 Processing helix chain '5' and resid 562 through 570 Processing helix chain '5' and resid 586 through 592 Processing helix chain '5' and resid 598 through 611 Processing helix chain '5' and resid 617 through 626 Processing helix chain '5' and resid 629 through 635 Processing helix chain '5' and resid 641 through 655 Processing helix chain '5' and resid 660 through 668 Processing helix chain '5' and resid 693 through 701 Processing helix chain '5' and resid 707 through 725 removed outlier: 3.944A pdb=" N ALA 5 725 " --> pdb=" O VAL 5 721 " (cutoff:3.500A) Processing helix chain '5' and resid 728 through 736 Processing helix chain '5' and resid 739 through 748 Processing helix chain '5' and resid 762 through 774 Processing helix chain '5' and resid 874 through 886 Processing helix chain '5' and resid 888 through 897 removed outlier: 3.725A pdb=" N ILE 5 896 " --> pdb=" O VAL 5 892 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR 5 897 " --> pdb=" O ARG 5 893 " (cutoff:3.500A) Processing helix chain '5' and resid 901 through 918 Processing helix chain '8' and resid 36 through 52 removed outlier: 3.982A pdb=" N TYR 8 46 " --> pdb=" O GLN 8 42 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA 8 48 " --> pdb=" O ALA 8 44 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N MET 8 49 " --> pdb=" O LYS 8 45 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY 8 50 " --> pdb=" O TYR 8 46 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU 8 51 " --> pdb=" O SER 8 47 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU 8 52 " --> pdb=" O ALA 8 48 " (cutoff:3.500A) Processing helix chain '8' and resid 89 through 99 Processing helix chain '8' and resid 103 through 112 Processing helix chain '8' and resid 119 through 129 Processing helix chain '8' and resid 131 through 142 Processing helix chain '8' and resid 147 through 156 Processing helix chain '8' and resid 159 through 163 Processing helix chain '8' and resid 194 through 209 Processing helix chain '8' and resid 221 through 239 removed outlier: 4.337A pdb=" N ALA 8 235 " --> pdb=" O GLN 8 231 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE 8 236 " --> pdb=" O ASN 8 232 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS 8 237 " --> pdb=" O LYS 8 233 " (cutoff:3.500A) Processing helix chain '8' and resid 243 through 256 Processing helix chain '8' and resid 274 through 278 Processing helix chain '8' and resid 281 through 307 Proline residue: 8 300 - end of helix Processing helix chain '8' and resid 353 through 356 No H-bonds generated for 'chain '8' and resid 353 through 356' Processing helix chain '8' and resid 395 through 402 removed outlier: 3.817A pdb=" N GLU 8 401 " --> pdb=" O ASN 8 397 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU 8 402 " --> pdb=" O GLN 8 398 " (cutoff:3.500A) Processing helix chain '8' and resid 418 through 423 Processing helix chain '8' and resid 428 through 445 Processing helix chain '1' and resid 7 through 16 Processing helix chain '1' and resid 20 through 23 No H-bonds generated for 'chain '1' and resid 20 through 23' Processing helix chain '1' and resid 27 through 38 Processing helix chain '1' and resid 70 through 80 Processing helix chain '1' and resid 108 through 115 Processing helix chain '1' and resid 317 through 321 Processing helix chain '1' and resid 497 through 502 Processing helix chain '1' and resid 597 through 612 removed outlier: 3.692A pdb=" N TRP 1 604 " --> pdb=" O TYR 1 600 " (cutoff:3.500A) Processing helix chain '1' and resid 709 through 724 Processing helix chain '1' and resid 728 through 741 Processing helix chain '1' and resid 752 through 776 Processing helix chain '1' and resid 916 through 931 Processing helix chain '1' and resid 945 through 948 No H-bonds generated for 'chain '1' and resid 945 through 948' Processing helix chain '1' and resid 951 through 956 removed outlier: 3.894A pdb=" N LEU 1 956 " --> pdb=" O ASP 1 952 " (cutoff:3.500A) Processing helix chain '9' and resid 188 through 200 Processing helix chain '9' and resid 209 through 213 Processing helix chain '9' and resid 225 through 239 Processing helix chain '9' and resid 244 through 253 Processing helix chain '9' and resid 263 through 278 removed outlier: 3.661A pdb=" N ILE 9 273 " --> pdb=" O SER 9 269 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LYS 9 276 " --> pdb=" O LEU 9 272 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TYR 9 277 " --> pdb=" O ILE 9 273 " (cutoff:3.500A) Processing helix chain '9' and resid 304 through 313 Processing helix chain '9' and resid 345 through 350 Processing helix chain '9' and resid 354 through 370 Processing helix chain '4' and resid 196 through 200 removed outlier: 4.877A pdb=" N TRP 4 200 " --> pdb=" O LEU 4 196 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 196 through 200' Processing helix chain '4' and resid 206 through 210 removed outlier: 4.118A pdb=" N LYS 4 210 " --> pdb=" O LEU 4 206 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 206 through 210' Processing helix chain '4' and resid 213 through 221 Processing helix chain '4' and resid 224 through 229 removed outlier: 3.865A pdb=" N GLN 4 228 " --> pdb=" O PRO 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 278 removed outlier: 4.127A pdb=" N LYS 4 277 " --> pdb=" O PHE 4 273 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN 4 278 " --> pdb=" O SER 4 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 337 through 340 removed outlier: 6.113A pdb=" N HIS 1 346 " --> pdb=" O SER 1 340 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR 1 345 " --> pdb=" O THR 1 585 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR 1 585 " --> pdb=" O THR 1 345 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN 1 581 " --> pdb=" O PRO 1 349 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER 1 582 " --> pdb=" O LEU 1 409 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR 1 400 " --> pdb=" O PHE 1 545 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR 1 404 " --> pdb=" O CYS 1 541 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 1 408 " --> pdb=" O ASP 1 537 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP 1 537 " --> pdb=" O VAL 1 408 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY 1 548 " --> pdb=" O ASP 1 565 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 386 through 390 removed outlier: 4.018A pdb=" N ILE 1 424 " --> pdb=" O TYR 1 512 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY 1 511 " --> pdb=" O THR 1 520 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 1 518 " --> pdb=" O CYS 1 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '5' and resid 213 through 219 removed outlier: 5.073A pdb=" N LEU 5 213 " --> pdb=" O PHE 1 104 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE 1 98 " --> pdb=" O LEU 5 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '8' and resid 31 through 34 removed outlier: 3.785A pdb=" N LYS 8 32 " --> pdb=" O GLN 8 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 126 through 135 removed outlier: 4.681A pdb=" N MET 4 127 " --> pdb=" O LEU 4 146 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU 4 146 " --> pdb=" O MET 4 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY 4 131 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 4 142 " --> pdb=" O GLY 4 131 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL 4 142 " --> pdb=" O ARG 4 170 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG 4 170 " --> pdb=" O VAL 4 142 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL 4 144 " --> pdb=" O SER 4 168 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER 4 168 " --> pdb=" O VAL 4 144 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU 4 146 " --> pdb=" O PHE 4 166 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE 4 166 " --> pdb=" O LEU 4 146 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS 4 162 " --> pdb=" O ASP 4 150 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR 4 181 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N SER 4 180 " --> pdb=" O LEU 4 297 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU 4 297 " --> pdb=" O SER 4 180 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N TYR 4 182 " --> pdb=" O LYS 4 295 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE 4 289 " --> pdb=" O VAL 4 188 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ARG 4 286 " --> pdb=" O GLN 4 322 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP 4 292 " --> pdb=" O TYR 4 316 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU 4 294 " --> pdb=" O GLY 4 314 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY 4 314 " --> pdb=" O GLU 4 294 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE 4 330 " --> pdb=" O TYR 4 317 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN 4 326 " --> pdb=" O ASP 4 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 4 327 " --> pdb=" O LEU 4 344 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN 4 340 " --> pdb=" O TYR 4 331 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 6.26 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: 4547 1.34 - 1.46: 3291 1.46 - 1.58: 6804 1.58 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 14745 Sorted by residual: bond pdb=" CA PHE 4 339 " pdb=" CB PHE 4 339 " ideal model delta sigma weight residual 1.527 1.560 -0.033 2.48e-02 1.63e+03 1.72e+00 bond pdb=" CG1 ILE 1 539 " pdb=" CD1 ILE 1 539 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" C LEU 9 205 " pdb=" N PRO 9 206 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.30e+00 bond pdb=" CG GLU 8 249 " pdb=" CD GLU 8 249 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" CG1 ILE 8 203 " pdb=" CD1 ILE 8 203 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.50e-01 ... (remaining 14740 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.88: 238 105.88 - 112.93: 8000 112.93 - 119.99: 5060 119.99 - 127.05: 6567 127.05 - 134.10: 139 Bond angle restraints: 20004 Sorted by residual: angle pdb=" N VAL 5 48 " pdb=" CA VAL 5 48 " pdb=" C VAL 5 48 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" C LEU 8 248 " pdb=" N GLU 8 249 " pdb=" CA GLU 8 249 " ideal model delta sigma weight residual 121.14 115.08 6.06 1.75e+00 3.27e-01 1.20e+01 angle pdb=" N GLU 8 249 " pdb=" CA GLU 8 249 " pdb=" CB GLU 8 249 " ideal model delta sigma weight residual 110.40 115.68 -5.28 1.63e+00 3.76e-01 1.05e+01 angle pdb=" C LYS 5 202 " pdb=" N ILE 5 203 " pdb=" CA ILE 5 203 " ideal model delta sigma weight residual 122.35 118.67 3.68 1.18e+00 7.18e-01 9.71e+00 angle pdb=" CA GLU 4 192 " pdb=" CB GLU 4 192 " pdb=" CG GLU 4 192 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.09e+00 ... (remaining 19999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 7859 17.69 - 35.39: 746 35.39 - 53.08: 132 53.08 - 70.78: 23 70.78 - 88.47: 9 Dihedral angle restraints: 8769 sinusoidal: 3293 harmonic: 5476 Sorted by residual: dihedral pdb=" CA PHE 8 423 " pdb=" C PHE 8 423 " pdb=" N PRO 8 424 " pdb=" CA PRO 8 424 " ideal model delta harmonic sigma weight residual 180.00 150.46 29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR 5 271 " pdb=" C TYR 5 271 " pdb=" N HIS 5 272 " pdb=" CA HIS 5 272 " ideal model delta harmonic sigma weight residual -180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CB CYS 5 656 " pdb=" SG CYS 5 656 " pdb=" SG CYS 4 357 " pdb=" CB CYS 4 357 " ideal model delta sinusoidal sigma weight residual -86.00 -127.09 41.09 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 8766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1695 0.043 - 0.086: 517 0.086 - 0.130: 110 0.130 - 0.173: 8 0.173 - 0.216: 1 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CA GLU 8 249 " pdb=" N GLU 8 249 " pdb=" C GLU 8 249 " pdb=" CB GLU 8 249 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA TYR 5 360 " pdb=" N TYR 5 360 " pdb=" C TYR 5 360 " pdb=" CB TYR 5 360 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ILE 5 216 " pdb=" N ILE 5 216 " pdb=" C ILE 5 216 " pdb=" CB ILE 5 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 2328 not shown) Planarity restraints: 2500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE 8 423 " 0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO 8 424 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO 8 424 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO 8 424 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 8 89 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO 8 90 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO 8 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO 8 90 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET 8 245 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.14e+00 pdb=" C MET 8 245 " 0.035 2.00e-02 2.50e+03 pdb=" O MET 8 245 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN 8 246 " -0.012 2.00e-02 2.50e+03 ... (remaining 2497 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 132 2.64 - 3.21: 13454 3.21 - 3.77: 20994 3.77 - 4.34: 28216 4.34 - 4.90: 47880 Nonbonded interactions: 110676 Sorted by model distance: nonbonded pdb=" NH2 ARG 5 652 " pdb=" OG SER 4 358 " model vdw 2.079 2.520 nonbonded pdb=" OG1 THR 4 148 " pdb=" OG SER 4 164 " model vdw 2.158 2.440 nonbonded pdb=" OD1 ASP 4 216 " pdb=" OH TYR 4 317 " model vdw 2.167 2.440 nonbonded pdb=" OD1 ASP 1 9 " pdb=" OH TYR 1 34 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR 1 529 " pdb=" O GLY 1 560 " model vdw 2.264 2.440 ... (remaining 110671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 5.530 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 40.130 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.004 0.049 14745 Z= 0.257 Angle : 0.582 9.554 20004 Z= 0.322 Chirality : 0.042 0.216 2331 Planarity : 0.004 0.088 2500 Dihedral : 14.317 88.469 5190 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1787 helix: 1.55 (0.17), residues: 1010 sheet: -1.45 (0.46), residues: 124 loop : -1.88 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 9 210 HIS 0.009 0.001 HIS 5 272 PHE 0.027 0.002 PHE 8 423 TYR 0.014 0.001 TYR 4 182 ARG 0.006 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.899 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.2428 time to fit residues: 33.3487 Evaluate side-chains 72 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14745 Z= 0.188 Angle : 0.505 8.762 20004 Z= 0.263 Chirality : 0.039 0.139 2331 Planarity : 0.004 0.085 2500 Dihedral : 4.428 29.965 1958 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.33 % Allowed : 5.93 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1787 helix: 1.76 (0.17), residues: 1013 sheet: -1.39 (0.46), residues: 125 loop : -1.80 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 9 210 HIS 0.004 0.001 HIS 5 272 PHE 0.025 0.001 PHE 8 423 TYR 0.010 0.001 TYR 5 333 ARG 0.003 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.817 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.2216 time to fit residues: 30.0277 Evaluate side-chains 77 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 1.701 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1302 time to fit residues: 3.1472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 715 ASN 9 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14745 Z= 0.199 Angle : 0.491 8.909 20004 Z= 0.256 Chirality : 0.039 0.139 2331 Planarity : 0.004 0.083 2500 Dihedral : 4.332 30.060 1958 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.26 % Allowed : 8.37 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.55 (0.21), residues: 1787 helix: 1.86 (0.17), residues: 1011 sheet: -1.30 (0.47), residues: 124 loop : -1.78 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 PHE 0.023 0.001 PHE 8 423 TYR 0.010 0.001 TYR 5 333 ARG 0.003 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 1.884 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 0.2236 time to fit residues: 31.2730 Evaluate side-chains 76 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1349 time to fit residues: 2.8136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14745 Z= 0.183 Angle : 0.481 8.723 20004 Z= 0.251 Chirality : 0.039 0.137 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.240 30.085 1958 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.53 % Allowed : 10.35 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.62 (0.21), residues: 1787 helix: 1.92 (0.17), residues: 1011 sheet: -1.25 (0.47), residues: 124 loop : -1.75 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 PHE 0.022 0.001 PHE 8 423 TYR 0.010 0.001 TYR 9 234 ARG 0.003 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.846 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 84 average time/residue: 0.2131 time to fit residues: 30.6670 Evaluate side-chains 78 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1288 time to fit residues: 3.0508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 739 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14745 Z= 0.194 Angle : 0.482 8.919 20004 Z= 0.252 Chirality : 0.039 0.137 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.215 30.139 1958 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.66 % Allowed : 11.80 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.65 (0.21), residues: 1787 helix: 1.94 (0.17), residues: 1011 sheet: -1.21 (0.47), residues: 124 loop : -1.74 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 220 HIS 0.003 0.001 HIS 4 333 PHE 0.020 0.001 PHE 8 423 TYR 0.037 0.001 TYR 9 234 ARG 0.003 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.760 Fit side-chains outliers start: 10 outliers final: 1 residues processed: 87 average time/residue: 0.2169 time to fit residues: 31.6622 Evaluate side-chains 75 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1647 time to fit residues: 2.7612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14745 Z= 0.190 Angle : 0.480 8.929 20004 Z= 0.251 Chirality : 0.039 0.139 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.196 30.252 1958 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.33 % Allowed : 12.72 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.68 (0.21), residues: 1787 helix: 1.97 (0.17), residues: 1010 sheet: -1.17 (0.47), residues: 124 loop : -1.74 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 PHE 0.019 0.001 PHE 8 423 TYR 0.028 0.001 TYR 9 234 ARG 0.003 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.931 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.2224 time to fit residues: 30.1818 Evaluate side-chains 76 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1438 time to fit residues: 3.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14745 Z= 0.313 Angle : 0.543 10.235 20004 Z= 0.283 Chirality : 0.041 0.153 2331 Planarity : 0.004 0.084 2500 Dihedral : 4.452 30.030 1958 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.66 % Allowed : 13.58 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.51 (0.21), residues: 1787 helix: 1.82 (0.17), residues: 1011 sheet: -1.30 (0.47), residues: 124 loop : -1.78 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 4 220 HIS 0.005 0.001 HIS 1 558 PHE 0.017 0.002 PHE 8 423 TYR 0.027 0.002 TYR 9 234 ARG 0.004 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.677 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.2203 time to fit residues: 29.8816 Evaluate side-chains 76 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2089 time to fit residues: 3.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14745 Z= 0.191 Angle : 0.485 9.278 20004 Z= 0.254 Chirality : 0.039 0.141 2331 Planarity : 0.004 0.082 2500 Dihedral : 4.270 29.983 1958 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.46 % Allowed : 13.65 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1787 helix: 1.92 (0.17), residues: 1013 sheet: -1.14 (0.47), residues: 124 loop : -1.75 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 9 210 HIS 0.003 0.001 HIS 4 333 PHE 0.018 0.001 PHE 8 423 TYR 0.024 0.001 TYR 9 234 ARG 0.002 0.000 ARG 5 609 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.887 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 78 average time/residue: 0.2223 time to fit residues: 29.7518 Evaluate side-chains 76 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1355 time to fit residues: 2.7466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9980 chunk 168 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 chunk 128 optimal weight: 0.0020 chunk 50 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14745 Z= 0.119 Angle : 0.447 8.606 20004 Z= 0.234 Chirality : 0.037 0.135 2331 Planarity : 0.003 0.080 2500 Dihedral : 3.953 30.240 1958 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.87 (0.21), residues: 1787 helix: 2.13 (0.17), residues: 1010 sheet: -1.12 (0.46), residues: 134 loop : -1.66 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.002 0.000 HIS 8 209 PHE 0.020 0.001 PHE 8 423 TYR 0.022 0.001 TYR 9 234 ARG 0.002 0.000 ARG 1 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.943 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2249 time to fit residues: 29.6334 Evaluate side-chains 76 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 0.0670 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 144 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14745 Z= 0.162 Angle : 0.467 10.725 20004 Z= 0.242 Chirality : 0.038 0.137 2331 Planarity : 0.004 0.081 2500 Dihedral : 3.973 30.366 1958 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.13 % Allowed : 14.50 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.89 (0.21), residues: 1787 helix: 2.13 (0.17), residues: 1009 sheet: -1.12 (0.46), residues: 134 loop : -1.62 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS 1 558 PHE 0.019 0.001 PHE 8 257 TYR 0.023 0.001 TYR 9 234 ARG 0.002 0.000 ARG 5 609 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.794 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.2212 time to fit residues: 29.2140 Evaluate side-chains 75 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 148 optimal weight: 0.0770 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069491 restraints weight = 37045.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.071079 restraints weight = 22582.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072159 restraints weight = 16268.586| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14745 Z= 0.168 Angle : 0.476 11.925 20004 Z= 0.249 Chirality : 0.038 0.227 2331 Planarity : 0.004 0.082 2500 Dihedral : 3.993 30.293 1958 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.13 % Rotamer: Outliers : 0.07 % Allowed : 14.50 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: 0.90 (0.21), residues: 1787 helix: 2.13 (0.17), residues: 1010 sheet: -1.11 (0.46), residues: 134 loop : -1.59 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 9 210 HIS 0.003 0.001 HIS 1 558 PHE 0.019 0.001 PHE 8 423 TYR 0.023 0.001 TYR 9 234 ARG 0.002 0.000 ARG 5 609 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.23 seconds wall clock time: 40 minutes 50.09 seconds (2450.09 seconds total)