Starting phenix.real_space_refine on Sun Dec 10 08:11:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ly9_30015/12_2023/6ly9_30015.pdb" } resolution = 3.93 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 9016 2.51 5 N 2431 2.21 5 O 2418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N GLU 99": "OE1" <-> "OE2" Residue "N ARG 158": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "N GLU 186": "OE1" <-> "OE2" Residue "N ARG 196": "NH1" <-> "NH2" Residue "N GLU 201": "OE1" <-> "OE2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N GLU 215": "OE1" <-> "OE2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ARG 229": "NH1" <-> "NH2" Residue "N ARG 255": "NH1" <-> "NH2" Residue "N GLU 268": "OE1" <-> "OE2" Residue "N ARG 273": "NH1" <-> "NH2" Residue "N GLU 291": "OE1" <-> "OE2" Residue "N ARG 296": "NH1" <-> "NH2" Residue "N ARG 316": "NH1" <-> "NH2" Residue "N ARG 385": "NH1" <-> "NH2" Residue "N GLU 426": "OE1" <-> "OE2" Residue "N GLU 433": "OE1" <-> "OE2" Residue "N ARG 543": "NH1" <-> "NH2" Residue "N ARG 563": "NH1" <-> "NH2" Residue "N ARG 588": "NH1" <-> "NH2" Residue "N ARG 622": "NH1" <-> "NH2" Residue "N GLU 627": "OE1" <-> "OE2" Residue "N ARG 643": "NH1" <-> "NH2" Residue "N ARG 649": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "T ARG 12": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "U ARG 12": "NH1" <-> "NH2" Residue "U ARG 36": "NH1" <-> "NH2" Residue "V ARG 12": "NH1" <-> "NH2" Residue "V GLU 63": "OE1" <-> "OE2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "Y ARG 12": "NH1" <-> "NH2" Residue "Z ARG 36": "NH1" <-> "NH2" Residue "M ARG 13": "NH1" <-> "NH2" Residue "M ARG 15": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M ARG 120": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M GLU 199": "OE1" <-> "OE2" Residue "M ARG 223": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 263": "NH1" <-> "NH2" Residue "M GLU 292": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13888 Number of models: 1 Model: "" Number of chains: 16 Chain: "N" Number of atoms: 5083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5083 Classifications: {'peptide': 649} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 613} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 523 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 510 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 513 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 511 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 503 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 513 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 507 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2522 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 88 Classifications: {'peptide': 22} Incomplete info: {'backbone_only': 21} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 80 Classifications: {'peptide': 20} Incomplete info: {'backbone_only': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 7.07, per 1000 atoms: 0.51 Number of scatterers: 13888 At special positions: 0 Unit cell: (140.8, 128.7, 115.5, 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 23 16.00 O 2418 8.00 N 2431 7.00 C 9016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " 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: 6.17 Conformation dependent library (CDL) restraints added in 2.8 seconds 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3206 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 81.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 32 removed outlier: 3.891A pdb=" N VAL N 30 " --> pdb=" O GLN N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 71 removed outlier: 4.230A pdb=" N ALA N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 129 Proline residue: N 93 - end of helix removed outlier: 4.454A pdb=" N GLU N 120 " --> pdb=" O GLN N 116 " (cutoff:3.500A) Proline residue: N 121 - end of helix Processing helix chain 'N' and resid 148 through 161 removed outlier: 4.049A pdb=" N LEU N 152 " --> pdb=" O LYS N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 198 removed outlier: 3.583A pdb=" N ALA N 192 " --> pdb=" O ASP N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 244 Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 245 through 270 removed outlier: 3.556A pdb=" N LEU N 249 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 297 removed outlier: 3.890A pdb=" N HIS N 297 " --> pdb=" O ALA N 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 330 No H-bonds generated for 'chain 'N' and resid 328 through 330' Processing helix chain 'N' and resid 331 through 336 removed outlier: 4.167A pdb=" N PHE N 336 " --> pdb=" O LEU N 332 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 363 removed outlier: 4.175A pdb=" N VAL N 353 " --> pdb=" O PRO N 349 " (cutoff:3.500A) Proline residue: N 356 - end of helix Processing helix chain 'N' and resid 364 through 385 removed outlier: 5.166A pdb=" N LEU N 370 " --> pdb=" O ILE N 366 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU N 371 " --> pdb=" O GLY N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 399 through 425 removed outlier: 4.277A pdb=" N LYS N 405 " --> pdb=" O GLN N 401 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL N 422 " --> pdb=" O VAL N 418 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE N 423 " --> pdb=" O VAL N 419 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 434 Processing helix chain 'N' and resid 459 through 489 Processing helix chain 'N' and resid 491 through 517 Processing helix chain 'N' and resid 524 through 543 Processing helix chain 'N' and resid 546 through 560 removed outlier: 4.313A pdb=" N PHE N 552 " --> pdb=" O ILE N 548 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR N 553 " --> pdb=" O PRO N 549 " (cutoff:3.500A) Processing helix chain 'N' and resid 561 through 589 removed outlier: 4.258A pdb=" N TYR N 565 " --> pdb=" O HIS N 561 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY N 568 " --> pdb=" O ILE N 564 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 626 removed outlier: 5.389A pdb=" N LEU N 614 " --> pdb=" O LEU N 610 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY N 615 " --> pdb=" O LEU N 611 " (cutoff:3.500A) Proline residue: N 620 - end of helix Processing helix chain 'N' and resid 628 through 633 removed outlier: 4.043A pdb=" N PHE N 632 " --> pdb=" O PHE N 628 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 46 removed outlier: 3.663A pdb=" N VAL O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG O 36 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing helix chain 'O' and resid 51 through 61 removed outlier: 3.537A pdb=" N ILE O 57 " --> pdb=" O GLY O 53 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 79 Processing helix chain 'P' and resid 8 through 46 removed outlier: 3.796A pdb=" N ARG P 36 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 46 " --> pdb=" O VAL P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 51 through 61 Processing helix chain 'P' and resid 63 through 80 Processing helix chain 'Q' and resid 8 through 47 removed outlier: 3.719A pdb=" N ALA Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 61 removed outlier: 3.775A pdb=" N ALA Q 55 " --> pdb=" O ASN Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 80 Processing helix chain 'R' and resid 10 through 48 removed outlier: 3.683A pdb=" N ILE R 15 " --> pdb=" O ASP R 11 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 61 Processing helix chain 'R' and resid 63 through 80 Processing helix chain 'S' and resid 8 through 48 Processing helix chain 'S' and resid 51 through 60 Processing helix chain 'S' and resid 63 through 78 removed outlier: 3.703A pdb=" N GLY S 78 " --> pdb=" O PHE S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 48 removed outlier: 3.539A pdb=" N ALA T 33 " --> pdb=" O GLY T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 61 removed outlier: 4.050A pdb=" N PHE T 58 " --> pdb=" O THR T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 80 removed outlier: 4.243A pdb=" N VAL T 66 " --> pdb=" O PRO T 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG T 79 " --> pdb=" O ILE T 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 48 removed outlier: 3.761A pdb=" N ALA U 16 " --> pdb=" O ARG U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 61 Processing helix chain 'U' and resid 62 through 79 removed outlier: 4.405A pdb=" N VAL U 66 " --> pdb=" O PRO U 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG U 79 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 46 removed outlier: 4.448A pdb=" N LEU V 14 " --> pdb=" O LEU V 10 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY V 43 " --> pdb=" O ALA V 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA V 46 " --> pdb=" O VAL V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 61 removed outlier: 3.571A pdb=" N GLY V 53 " --> pdb=" O ARG V 49 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 57 " --> pdb=" O GLY V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 79 removed outlier: 4.031A pdb=" N VAL V 66 " --> pdb=" O PRO V 62 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG V 79 " --> pdb=" O ILE V 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 8 through 48 removed outlier: 3.889A pdb=" N ARG W 36 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 60 removed outlier: 4.422A pdb=" N ILE W 57 " --> pdb=" O GLY W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 78 removed outlier: 4.167A pdb=" N VAL W 66 " --> pdb=" O PRO W 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 48 removed outlier: 3.799A pdb=" N GLY X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG X 36 " --> pdb=" O VAL X 32 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 61 removed outlier: 3.652A pdb=" N ILE X 57 " --> pdb=" O GLY X 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 78 Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.833A pdb=" N ALA Y 16 " --> pdb=" O ARG Y 12 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL Y 17 " --> pdb=" O GLY Y 13 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 61 Processing helix chain 'Y' and resid 64 through 80 removed outlier: 3.824A pdb=" N ARG Y 79 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Y 80 " --> pdb=" O LEU Y 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 48 removed outlier: 4.137A pdb=" N ARG Z 36 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU Z 47 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 60 removed outlier: 3.517A pdb=" N ALA Z 55 " --> pdb=" O ASN Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 79 removed outlier: 4.395A pdb=" N VAL Z 66 " --> pdb=" O PRO Z 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 18 removed outlier: 3.509A pdb=" N LEU M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY M 17 " --> pdb=" O ARG M 13 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 29 removed outlier: 4.268A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN M 26 " --> pdb=" O GLU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 43 removed outlier: 3.509A pdb=" N THR M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 49 Processing helix chain 'M' and resid 53 through 69 Processing helix chain 'M' and resid 71 through 76 removed outlier: 3.691A pdb=" N VAL M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 106 removed outlier: 3.555A pdb=" N ALA M 83 " --> pdb=" O GLU M 79 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 130 removed outlier: 3.858A pdb=" N TRP M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 Processing helix chain 'M' and resid 147 through 156 Processing helix chain 'M' and resid 160 through 184 removed outlier: 3.815A pdb=" N GLU M 165 " --> pdb=" O LEU M 161 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA M 166 " --> pdb=" O ALA M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 208 removed outlier: 3.533A pdb=" N PHE M 205 " --> pdb=" O LEU M 201 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 234 Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 257 through 275 Processing helix chain 'M' and resid 276 through 278 No H-bonds generated for 'chain 'M' and resid 276 through 278' Processing helix chain 'M' and resid 283 through 309 removed outlier: 3.801A pdb=" N ARG M 306 " --> pdb=" O LEU M 302 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 321 removed outlier: 4.257A pdb=" N VAL M 316 " --> pdb=" O PRO M 312 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU M 319 " --> pdb=" O GLN M 315 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL M 321 " --> pdb=" O GLU M 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 42 removed outlier: 3.590A pdb=" N LEU K 33 " --> pdb=" O LYS K 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 21 removed outlier: 4.509A pdb=" N ALA L 14 " --> pdb=" O GLN L 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU L 15 " --> pdb=" O GLU L 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'N' and resid 139 through 140 Processing sheet with id=AA3, first strand: chain 'N' and resid 318 through 319 Processing sheet with id=AA4, first strand: chain 'N' and resid 389 through 391 removed outlier: 3.534A pdb=" N LEU N 398 " --> pdb=" O LEU N 389 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE N 391 " --> pdb=" O LEU N 396 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU N 396 " --> pdb=" O ILE N 391 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3375 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: 4.32 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4642 1.34 - 1.46: 2968 1.46 - 1.58: 6451 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 14105 Sorted by residual: bond pdb=" CA ARG M 156 " pdb=" C ARG M 156 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.72e-02 3.38e+03 2.46e+00 bond pdb=" N LEU M 252 " pdb=" CA LEU M 252 " ideal model delta sigma weight residual 1.459 1.442 0.017 1.19e-02 7.06e+03 2.04e+00 bond pdb=" C ASP N 346 " pdb=" N PRO N 347 " ideal model delta sigma weight residual 1.331 1.320 0.011 7.90e-03 1.60e+04 1.97e+00 bond pdb=" CB TRP N 358 " pdb=" CG TRP N 358 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.94e+00 bond pdb=" CG1 ILE Z 37 " pdb=" CD1 ILE Z 37 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.93: 244 105.93 - 112.96: 7742 112.96 - 119.99: 5027 119.99 - 127.02: 5960 127.02 - 134.05: 112 Bond angle restraints: 19085 Sorted by residual: angle pdb=" N LEU M 252 " pdb=" CA LEU M 252 " pdb=" C LEU M 252 " ideal model delta sigma weight residual 111.07 104.63 6.44 1.07e+00 8.73e-01 3.63e+01 angle pdb=" N ASN P 51 " pdb=" CA ASN P 51 " pdb=" C ASN P 51 " ideal model delta sigma weight residual 114.12 107.87 6.25 1.39e+00 5.18e-01 2.02e+01 angle pdb=" N VAL N 334 " pdb=" CA VAL N 334 " pdb=" C VAL N 334 " ideal model delta sigma weight residual 113.71 109.58 4.13 9.50e-01 1.11e+00 1.89e+01 angle pdb=" C GLY M 251 " pdb=" N LEU M 252 " pdb=" CA LEU M 252 " ideal model delta sigma weight residual 120.44 115.72 4.72 1.30e+00 5.92e-01 1.32e+01 angle pdb=" N GLY M 254 " pdb=" CA GLY M 254 " pdb=" C GLY M 254 " ideal model delta sigma weight residual 110.56 115.90 -5.34 1.66e+00 3.63e-01 1.03e+01 ... (remaining 19080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7333 17.95 - 35.89: 716 35.89 - 53.84: 130 53.84 - 71.78: 20 71.78 - 89.73: 9 Dihedral angle restraints: 8208 sinusoidal: 3099 harmonic: 5109 Sorted by residual: dihedral pdb=" CA GLU N 426 " pdb=" C GLU N 426 " pdb=" N PHE N 427 " pdb=" CA PHE N 427 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 137 " pdb=" C PHE N 137 " pdb=" N LEU N 138 " pdb=" CA LEU N 138 " ideal model delta harmonic sigma weight residual 180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS N 434 " pdb=" C HIS N 434 " pdb=" N LEU N 435 " pdb=" CA LEU N 435 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1637 0.046 - 0.091: 532 0.091 - 0.137: 78 0.137 - 0.183: 6 0.183 - 0.228: 1 Chirality restraints: 2254 Sorted by residual: chirality pdb=" CG LEU N 435 " pdb=" CB LEU N 435 " pdb=" CD1 LEU N 435 " pdb=" CD2 LEU N 435 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TRP N 545 " pdb=" N TRP N 545 " pdb=" C TRP N 545 " pdb=" CB TRP N 545 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CB THR N 339 " pdb=" CA THR N 339 " pdb=" OG1 THR N 339 " pdb=" CG2 THR N 339 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2251 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER P 50 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C SER P 50 " 0.040 2.00e-02 2.50e+03 pdb=" O SER P 50 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN P 51 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY N 12 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO N 13 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO N 13 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 13 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE N 427 " -0.007 2.00e-02 2.50e+03 1.28e-02 2.86e+00 pdb=" CG PHE N 427 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE N 427 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE N 427 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE N 427 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE N 427 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE N 427 " 0.004 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1559 2.74 - 3.28: 16317 3.28 - 3.82: 24357 3.82 - 4.36: 28536 4.36 - 4.90: 46679 Nonbonded interactions: 117448 Sorted by model distance: nonbonded pdb=" O GLU N 627 " pdb=" NZ LYS N 631 " model vdw 2.195 2.520 nonbonded pdb=" O SER N 251 " pdb=" OG1 THR N 254 " model vdw 2.200 2.440 nonbonded pdb=" O HIS N 65 " pdb=" OG SER N 68 " model vdw 2.212 2.440 nonbonded pdb=" NH1 ARG N 482 " pdb=" O LYS N 631 " model vdw 2.213 2.520 nonbonded pdb=" NE2 GLN Q 34 " pdb=" O LEU Q 59 " model vdw 2.238 2.520 ... (remaining 117443 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 'O' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'P' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Q' and (resid 9 through 49 or (resid 50 and (name N or name CA or name C \ or name O )) or resid 51 through 80)) selection = (chain 'R' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'S' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 80)) selection = (chain 'T' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'U' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'V' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'W' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'X' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Y' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) selection = (chain 'Z' and (resid 9 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 49 or (resid 50 and (name N or name \ CA or name C or name O )) or resid 51 through 80)) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.460 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.270 Find NCS groups from input model: 0.740 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14105 Z= 0.381 Angle : 0.746 9.380 19085 Z= 0.408 Chirality : 0.042 0.228 2254 Planarity : 0.004 0.052 2456 Dihedral : 14.600 89.729 4999 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.05 % Allowed : 10.01 % Favored : 88.94 % 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: -3.45 (0.16), residues: 1862 helix: -1.76 (0.11), residues: 1443 sheet: -4.05 (0.68), residues: 40 loop : -3.42 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 545 HIS 0.007 0.001 HIS M 94 PHE 0.028 0.002 PHE N 427 TYR 0.014 0.002 TYR N 373 ARG 0.006 0.000 ARG N 622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 457 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 467 average time/residue: 0.2770 time to fit residues: 188.6717 Evaluate side-chains 383 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 373 time to evaluate : 1.501 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.1798 time to fit residues: 4.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 95 GLN N 97 HIS N 104 GLN N 106 GLN N 116 GLN N 183 HIS ** N 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 237 HIS N 554 GLN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 652 GLN O 77 ASN R 34 GLN R 51 ASN Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 126 GLN ** M 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14105 Z= 0.237 Angle : 0.705 10.309 19085 Z= 0.347 Chirality : 0.042 0.335 2254 Planarity : 0.005 0.098 2456 Dihedral : 4.806 24.991 2024 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.56 % Allowed : 20.93 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1862 helix: -0.09 (0.13), residues: 1451 sheet: -3.69 (0.73), residues: 40 loop : -2.81 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 545 HIS 0.006 0.001 HIS N 169 PHE 0.027 0.002 PHE S 68 TYR 0.024 0.002 TYR M 191 ARG 0.008 0.001 ARG M 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 435 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 61 outliers final: 34 residues processed: 460 average time/residue: 0.2429 time to fit residues: 165.1547 Evaluate side-chains 411 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 377 time to evaluate : 1.422 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 34 outliers final: 4 residues processed: 34 average time/residue: 0.1519 time to fit residues: 10.9360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 149 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 638 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 ASN M 126 GLN M 200 ASN ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14105 Z= 0.225 Angle : 0.691 9.333 19085 Z= 0.339 Chirality : 0.042 0.334 2254 Planarity : 0.005 0.053 2456 Dihedral : 4.658 25.034 2024 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.89 % Allowed : 23.32 % Favored : 72.80 % 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: -0.40 (0.19), residues: 1862 helix: 0.46 (0.13), residues: 1452 sheet: -3.29 (0.75), residues: 38 loop : -2.56 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.047 0.002 PHE S 68 TYR 0.024 0.001 TYR M 191 ARG 0.008 0.001 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 424 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 52 outliers final: 19 residues processed: 455 average time/residue: 0.2398 time to fit residues: 164.4773 Evaluate side-chains 389 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 370 time to evaluate : 1.534 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 4 residues processed: 19 average time/residue: 0.1278 time to fit residues: 6.6956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 183 HIS N 312 HIS ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14105 Z= 0.232 Angle : 0.691 9.005 19085 Z= 0.338 Chirality : 0.041 0.213 2254 Planarity : 0.005 0.052 2456 Dihedral : 4.582 24.483 2024 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.33 % Allowed : 25.49 % Favored : 70.18 % 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: -0.08 (0.19), residues: 1862 helix: 0.65 (0.13), residues: 1473 sheet: -3.25 (0.75), residues: 38 loop : -2.44 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 625 HIS 0.006 0.001 HIS N 65 PHE 0.058 0.002 PHE S 68 TYR 0.026 0.001 TYR M 191 ARG 0.010 0.000 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 407 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 435 average time/residue: 0.2476 time to fit residues: 160.9342 Evaluate side-chains 395 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 364 time to evaluate : 1.552 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 31 outliers final: 4 residues processed: 31 average time/residue: 0.1433 time to fit residues: 9.9464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14105 Z= 0.230 Angle : 0.705 10.303 19085 Z= 0.342 Chirality : 0.042 0.353 2254 Planarity : 0.005 0.091 2456 Dihedral : 4.549 25.377 2024 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.44 % Allowed : 27.73 % Favored : 68.83 % 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: 0.12 (0.20), residues: 1862 helix: 0.79 (0.13), residues: 1459 sheet: -3.44 (0.69), residues: 40 loop : -2.24 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.062 0.002 PHE S 68 TYR 0.027 0.001 TYR M 191 ARG 0.011 0.000 ARG N 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 411 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 437 average time/residue: 0.2440 time to fit residues: 161.2850 Evaluate side-chains 393 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 374 time to evaluate : 1.676 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 19 outliers final: 4 residues processed: 19 average time/residue: 0.1457 time to fit residues: 7.2431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14105 Z= 0.237 Angle : 0.745 11.780 19085 Z= 0.355 Chirality : 0.044 0.370 2254 Planarity : 0.005 0.068 2456 Dihedral : 4.567 24.768 2024 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.69 % Allowed : 30.79 % Favored : 66.52 % 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: 0.20 (0.20), residues: 1862 helix: 0.81 (0.13), residues: 1470 sheet: -2.88 (0.90), residues: 31 loop : -2.24 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP N 625 HIS 0.009 0.001 HIS N 65 PHE 0.075 0.002 PHE S 68 TYR 0.031 0.001 TYR M 191 ARG 0.010 0.000 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 407 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 426 average time/residue: 0.2112 time to fit residues: 138.2132 Evaluate side-chains 407 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 386 time to evaluate : 1.534 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 21 outliers final: 4 residues processed: 21 average time/residue: 0.1364 time to fit residues: 7.5671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 7.9990 chunk 110 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 25 GLN N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 ASN S 34 GLN ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14105 Z= 0.224 Angle : 0.730 10.516 19085 Z= 0.351 Chirality : 0.042 0.269 2254 Planarity : 0.005 0.076 2456 Dihedral : 4.549 24.578 2024 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.84 % Allowed : 32.14 % Favored : 65.02 % 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: 0.31 (0.20), residues: 1862 helix: 0.88 (0.13), residues: 1460 sheet: -2.77 (0.91), residues: 31 loop : -2.06 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.068 0.002 PHE S 68 TYR 0.031 0.001 TYR M 191 ARG 0.012 0.000 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 407 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 431 average time/residue: 0.2320 time to fit residues: 152.9291 Evaluate side-chains 393 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 376 time to evaluate : 1.491 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 17 outliers final: 4 residues processed: 17 average time/residue: 0.1322 time to fit residues: 6.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.0270 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 161 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14105 Z= 0.222 Angle : 0.769 15.487 19085 Z= 0.363 Chirality : 0.044 0.463 2254 Planarity : 0.005 0.056 2456 Dihedral : 4.531 23.145 2024 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.32 % Allowed : 33.78 % Favored : 63.90 % 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: 0.37 (0.20), residues: 1862 helix: 0.90 (0.13), residues: 1462 sheet: -2.84 (0.91), residues: 31 loop : -1.91 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.067 0.002 PHE V 68 TYR 0.033 0.001 TYR M 191 ARG 0.013 0.000 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 400 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 417 average time/residue: 0.2293 time to fit residues: 144.7992 Evaluate side-chains 396 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 378 time to evaluate : 1.513 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 18 outliers final: 4 residues processed: 18 average time/residue: 0.1291 time to fit residues: 6.4447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN R 34 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14105 Z= 0.239 Angle : 0.795 13.573 19085 Z= 0.377 Chirality : 0.046 0.427 2254 Planarity : 0.005 0.060 2456 Dihedral : 4.543 26.233 2024 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.27 % Allowed : 34.90 % Favored : 63.83 % 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: 0.36 (0.20), residues: 1862 helix: 0.87 (0.13), residues: 1462 sheet: -2.78 (0.91), residues: 31 loop : -1.83 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.070 0.002 PHE S 68 TYR 0.032 0.001 TYR M 191 ARG 0.013 0.000 ARG N 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 393 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 403 average time/residue: 0.2368 time to fit residues: 144.9698 Evaluate side-chains 383 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 373 time to evaluate : 1.617 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.1194 time to fit residues: 4.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 77 ASN Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14105 Z= 0.237 Angle : 0.797 13.162 19085 Z= 0.379 Chirality : 0.046 0.415 2254 Planarity : 0.005 0.062 2456 Dihedral : 4.584 28.730 2024 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.12 % Allowed : 35.13 % Favored : 63.75 % 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: 0.43 (0.20), residues: 1862 helix: 0.92 (0.13), residues: 1460 sheet: -2.74 (0.93), residues: 31 loop : -1.81 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP N 625 HIS 0.007 0.001 HIS N 65 PHE 0.068 0.002 PHE S 68 TYR 0.030 0.001 TYR M 191 ARG 0.014 0.000 ARG N 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 377 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 385 average time/residue: 0.2392 time to fit residues: 139.7851 Evaluate side-chains 380 residues out of total 1377 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 370 time to evaluate : 1.671 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "LEU T 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU W 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU X 80 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU Y 80 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.1297 time to fit residues: 4.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 386 ASN ** N 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN S 34 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 51 ASN ** Z 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093142 restraints weight = 33265.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.095795 restraints weight = 19197.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097404 restraints weight = 12906.440| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14105 Z= 0.270 Angle : 0.804 13.834 19085 Z= 0.384 Chirality : 0.046 0.370 2254 Planarity : 0.005 0.064 2456 Dihedral : 4.563 26.710 2024 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.97 % Allowed : 35.43 % Favored : 63.60 % 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: 0.42 (0.20), residues: 1862 helix: 0.92 (0.13), residues: 1457 sheet: -2.70 (0.93), residues: 31 loop : -1.82 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP N 625 HIS 0.008 0.001 HIS N 65 PHE 0.066 0.002 PHE S 68 TYR 0.030 0.001 TYR M 191 ARG 0.014 0.000 ARG N 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.88 seconds wall clock time: 60 minutes 56.37 seconds (3656.37 seconds total)