Starting phenix.real_space_refine (version: dev) on Wed Dec 14 17:54:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eau_27986/12_2022/8eau_27986.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.207 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "a GLU 24": "OE1" <-> "OE2" Residue "a ASP 109": "OD1" <-> "OD2" Residue "a GLU 219": "OE1" <-> "OE2" Residue "a GLU 254": "OE1" <-> "OE2" Residue "a ASP 498": "OD1" <-> "OD2" Residue "a GLU 526": "OE1" <-> "OE2" Residue "a ASP 623": "OD1" <-> "OD2" Residue "a PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 804": "OE1" <-> "OE2" Residue "b GLU 255": "OE1" <-> "OE2" Residue "c TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 199": "OE1" <-> "OE2" Residue "d GLU 319": "OE1" <-> "OE2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "f ASP 47": "OD1" <-> "OD2" Residue "g GLU 3": "OE1" <-> "OE2" Residue "g PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 157": "OD1" <-> "OD2" Residue "i GLU 3": "OE1" <-> "OE2" Residue "i TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 3": "OE1" <-> "OE2" Residue "k GLU 3": "OE1" <-> "OE2" Residue "k ASP 157": "OD1" <-> "OD2" Residue "l TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 137": "OE1" <-> "OE2" Residue "n GLU 3": "OE1" <-> "OE2" Residue "o TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 88": "OE1" <-> "OE2" Residue "o TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 21909 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5975 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 21, 'TRANS': 736} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 5, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 105 Chain: "b" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 363 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "c" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1483 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2523 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 82 Chain: "e" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 522 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "g" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1106 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1138 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "i" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1128 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1111 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "k" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1104 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "m" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1111 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1084 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "o" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1133 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "p" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 425 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Time building chain proxies: 14.67, per 1000 atoms: 0.67 Number of scatterers: 21909 At special positions: 0 Unit cell: (122.57, 114.33, 132.87, 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 130 16.00 O 3870 8.00 N 3520 7.00 C 14389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.65 Conformation dependent library (CDL) restraints added in 3.6 seconds 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5312 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 6 sheets defined 80.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'a' and resid 25 through 37 Processing helix chain 'a' and resid 49 through 53 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 87 through 93 Processing helix chain 'a' and resid 105 through 146 removed outlier: 3.567A pdb=" N GLU a 119 " --> pdb=" O SER a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 207 removed outlier: 4.333A pdb=" N THR a 198 " --> pdb=" O ASP a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 255 removed outlier: 3.576A pdb=" N SER a 255 " --> pdb=" O LYS a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 324 removed outlier: 3.876A pdb=" N THR a 290 " --> pdb=" O THR a 286 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 361 Processing helix chain 'a' and resid 387 through 395 Processing helix chain 'a' and resid 407 through 424 removed outlier: 4.415A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 425 through 441 removed outlier: 3.624A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 442 through 447 Processing helix chain 'a' and resid 453 through 461 Processing helix chain 'a' and resid 461 through 479 Processing helix chain 'a' and resid 519 through 523 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.637A pdb=" N PHE a 531 " --> pdb=" O ASN a 527 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 571 Processing helix chain 'a' and resid 571 through 596 removed outlier: 4.768A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 597 through 602 Processing helix chain 'a' and resid 607 through 618 removed outlier: 3.947A pdb=" N PHE a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 629 through 660 removed outlier: 3.707A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 4.711A pdb=" N LYS a 652 " --> pdb=" O LEU a 648 " (cutoff:3.500A) Proline residue: a 653 - end of helix Processing helix chain 'a' and resid 711 through 733 removed outlier: 3.771A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) Processing helix chain 'a' and resid 734 through 755 Processing helix chain 'a' and resid 757 through 761 Processing helix chain 'a' and resid 763 through 784 Processing helix chain 'a' and resid 789 through 803 Processing helix chain 'a' and resid 805 through 810 removed outlier: 4.150A pdb=" N PHE a 809 " --> pdb=" O SER a 805 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 831 Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'b' and resid 250 through 254 removed outlier: 3.682A pdb=" N ALA b 253 " --> pdb=" O THR b 250 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 39 Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 90 removed outlier: 3.859A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 92 No H-bonds generated for 'chain 'c' and resid 91 through 92' Processing helix chain 'c' and resid 93 through 94 No H-bonds generated for 'chain 'c' and resid 93 through 94' Processing helix chain 'c' and resid 95 through 123 removed outlier: 3.665A pdb=" N LYS c 99 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 133 Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 180 through 208 removed outlier: 4.043A pdb=" N ILE c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS c 208 " --> pdb=" O LEU c 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 removed outlier: 3.799A pdb=" N PHE d 6 " --> pdb=" O GLU d 2 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN d 7 " --> pdb=" O GLY d 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 2 through 7' Processing helix chain 'd' and resid 9 through 23 removed outlier: 4.586A pdb=" N ILE d 13 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 35 Processing helix chain 'd' and resid 38 through 48 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 88 through 111 removed outlier: 3.583A pdb=" N ARG d 92 " --> pdb=" O SER d 88 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 132 Processing helix chain 'd' and resid 136 through 142 Processing helix chain 'd' and resid 144 through 146 No H-bonds generated for 'chain 'd' and resid 144 through 146' Processing helix chain 'd' and resid 147 through 152 Processing helix chain 'd' and resid 153 through 156 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 201 through 228 Processing helix chain 'd' and resid 236 through 241 Processing helix chain 'd' and resid 250 through 259 Processing helix chain 'd' and resid 261 through 270 Processing helix chain 'd' and resid 283 through 301 removed outlier: 3.680A pdb=" N THR d 301 " --> pdb=" O ARG d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.009A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 338 Processing helix chain 'e' and resid 4 through 25 removed outlier: 3.586A pdb=" N VAL e 8 " --> pdb=" O PHE e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 55 removed outlier: 4.581A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN e 55 " --> pdb=" O THR e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 72 Processing helix chain 'f' and resid 6 through 33 Processing helix chain 'f' and resid 35 through 40 Processing helix chain 'f' and resid 47 through 72 removed outlier: 3.597A pdb=" N VAL f 51 " --> pdb=" O ASP f 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL g 44 " --> pdb=" O CYS g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 48 No H-bonds generated for 'chain 'g' and resid 46 through 48' Processing helix chain 'g' and resid 49 through 54 Processing helix chain 'g' and resid 54 through 76 Processing helix chain 'g' and resid 83 through 122 Processing helix chain 'g' and resid 124 through 152 removed outlier: 4.423A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 44 removed outlier: 4.196A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL h 44 " --> pdb=" O CYS h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 48 No H-bonds generated for 'chain 'h' and resid 46 through 48' Processing helix chain 'h' and resid 49 through 54 removed outlier: 3.518A pdb=" N ILE h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 77 Processing helix chain 'h' and resid 83 through 120 Processing helix chain 'h' and resid 124 through 154 removed outlier: 4.372A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 44 removed outlier: 4.296A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 48 No H-bonds generated for 'chain 'i' and resid 46 through 48' Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 78 removed outlier: 3.608A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA i 64 " --> pdb=" O ALA i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 83 through 122 removed outlier: 4.039A pdb=" N ARG i 117 " --> pdb=" O ASP i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 155 removed outlier: 4.140A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR i 155 " --> pdb=" O ASN i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR j 42 " --> pdb=" O GLY j 38 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 78 Processing helix chain 'j' and resid 83 through 120 removed outlier: 3.729A pdb=" N SER j 120 " --> pdb=" O VAL j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 124 through 154 removed outlier: 4.316A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.337A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 45 No H-bonds generated for 'chain 'k' and resid 44 through 45' Processing helix chain 'k' and resid 46 through 48 No H-bonds generated for 'chain 'k' and resid 46 through 48' Processing helix chain 'k' and resid 49 through 54 Processing helix chain 'k' and resid 54 through 76 Processing helix chain 'k' and resid 83 through 122 removed outlier: 3.871A pdb=" N ARG k 117 " --> pdb=" O ASP k 113 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 153 removed outlier: 3.960A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 46 removed outlier: 4.232A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL l 44 " --> pdb=" O CYS l 40 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU l 45 " --> pdb=" O ALA l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 54 Processing helix chain 'l' and resid 54 through 76 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.592A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 153 removed outlier: 4.452A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY l 143 " --> pdb=" O LEU l 139 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 40 removed outlier: 4.062A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 44 removed outlier: 3.776A pdb=" N VAL m 44 " --> pdb=" O ALA m 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 41 through 44' Processing helix chain 'm' and resid 45 through 49 removed outlier: 3.724A pdb=" N ASP m 48 " --> pdb=" O LEU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 83 through 122 Processing helix chain 'm' and resid 124 through 153 removed outlier: 4.572A pdb=" N GLY m 128 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 37 removed outlier: 4.340A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 46 removed outlier: 4.131A pdb=" N LEU n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 78 removed outlier: 4.373A pdb=" N VAL n 57 " --> pdb=" O ASN n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 118 Processing helix chain 'n' and resid 123 through 153 removed outlier: 5.426A pdb=" N ILE n 130 " --> pdb=" O PHE n 126 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU n 131 " --> pdb=" O VAL n 127 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE n 132 " --> pdb=" O GLY n 128 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 3.943A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY o 44 " --> pdb=" O LYS o 40 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY o 47 " --> pdb=" O ILE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 60 through 83 removed outlier: 3.543A pdb=" N ASN o 83 " --> pdb=" O LEU o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 128 removed outlier: 4.370A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 163 removed outlier: 4.035A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 35 removed outlier: 3.741A pdb=" N MET p 14 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Proline residue: p 24 - end of helix Processing helix chain 'p' and resid 37 through 63 Processing sheet with id=AA1, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'a' and resid 40 through 41 removed outlier: 4.183A pdb=" N LEU a 16 " --> pdb=" O LEU a 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 213 through 217 removed outlier: 4.103A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA6, first strand: chain 'a' and resid 506 through 507 1813 hydrogen bonds defined for protein. 5319 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: 7.27 Time building geometry restraints manager: 10.34 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: 6690 1.34 - 1.46: 3449 1.46 - 1.58: 12011 1.58 - 1.70: 0 1.70 - 1.81: 201 Bond restraints: 22351 Sorted by residual: bond pdb=" CB VAL c 110 " pdb=" CG1 VAL c 110 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CB CYS a 589 " pdb=" SG CYS a 589 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CB GLN m 90 " pdb=" CG GLN m 90 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB ILE g 62 " pdb=" CG2 ILE g 62 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CG LEU g 141 " pdb=" CD1 LEU g 141 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 22346 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.51: 309 104.51 - 111.88: 10948 111.88 - 119.25: 7244 119.25 - 126.62: 11679 126.62 - 133.98: 217 Bond angle restraints: 30397 Sorted by residual: angle pdb=" C ASN d 333 " pdb=" CA ASN d 333 " pdb=" CB ASN d 333 " ideal model delta sigma weight residual 116.63 111.08 5.55 1.16e+00 7.43e-01 2.29e+01 angle pdb=" C ILE c 79 " pdb=" N PHE c 80 " pdb=" CA PHE c 80 " ideal model delta sigma weight residual 120.68 113.82 6.86 1.70e+00 3.46e-01 1.63e+01 angle pdb=" C ILE k 54 " pdb=" N VAL k 55 " pdb=" CA VAL k 55 " ideal model delta sigma weight residual 120.33 123.37 -3.04 8.00e-01 1.56e+00 1.45e+01 angle pdb=" CA GLY k 79 " pdb=" C GLY k 79 " pdb=" N GLN k 80 " ideal model delta sigma weight residual 114.58 117.60 -3.02 8.60e-01 1.35e+00 1.23e+01 angle pdb=" CB MET c 58 " pdb=" CG MET c 58 " pdb=" SD MET c 58 " ideal model delta sigma weight residual 112.70 123.18 -10.48 3.00e+00 1.11e-01 1.22e+01 ... (remaining 30392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12000 17.98 - 35.95: 783 35.95 - 53.93: 119 53.93 - 71.91: 20 71.91 - 89.89: 16 Dihedral angle restraints: 12938 sinusoidal: 4583 harmonic: 8355 Sorted by residual: dihedral pdb=" CA LEU a 256 " pdb=" C LEU a 256 " pdb=" N ASP a 257 " pdb=" CA ASP a 257 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU a 254 " pdb=" C GLU a 254 " pdb=" N SER a 255 " pdb=" CA SER a 255 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE a 423 " pdb=" C PHE a 423 " pdb=" N GLY a 424 " pdb=" CA GLY a 424 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 12935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2274 0.033 - 0.066: 952 0.066 - 0.100: 341 0.100 - 0.133: 82 0.133 - 0.166: 12 Chirality restraints: 3661 Sorted by residual: chirality pdb=" CG LEU a 211 " pdb=" CB LEU a 211 " pdb=" CD1 LEU a 211 " pdb=" CD2 LEU a 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA PHE c 80 " pdb=" N PHE c 80 " pdb=" C PHE c 80 " pdb=" CB PHE c 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB THR a 621 " pdb=" CA THR a 621 " pdb=" OG1 THR a 621 " pdb=" CG2 THR a 621 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 3658 not shown) Planarity restraints: 3770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR d 249 " 0.052 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO d 250 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO d 250 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO d 250 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 80 " 0.027 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE c 80 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE c 80 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE c 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE c 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 80 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE c 80 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG k 46 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO k 47 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO k 47 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO k 47 " 0.042 5.00e-02 4.00e+02 ... (remaining 3767 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 185 2.66 - 3.22: 22907 3.22 - 3.78: 36962 3.78 - 4.34: 50941 4.34 - 4.90: 82707 Nonbonded interactions: 193702 Sorted by model distance: nonbonded pdb=" OG SER m 77 " pdb=" OE1 GLN m 90 " model vdw 2.097 2.440 nonbonded pdb=" OE2 GLU d 14 " pdb=" NH1 ARG d 18 " model vdw 2.205 2.520 nonbonded pdb=" OE1 GLN d 86 " pdb=" NH1 ARG g 117 " model vdw 2.209 2.520 nonbonded pdb=" NZ LYS a 251 " pdb=" O VAL d 141 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR i 66 " pdb=" OE2 GLU i 137 " model vdw 2.219 2.440 ... (remaining 193697 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 'g' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'h' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'i' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'j' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 through 115 or (r \ esid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 t \ hrough 118 or (resid 119 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 155)) selection = (chain 'k' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 through 52 or (re \ sid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) o \ r resid 125 through 155)) selection = (chain 'l' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'm' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 155)) selection = (chain 'n' and (resid 2 through 51 or (resid 52 through 53 and (name N or name C \ A or name C or name O or name CB )) or resid 54 through 115 or (resid 116 and (n \ ame N or name CA or name C or name O or name CB )) or resid 117 through 155)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 14389 2.51 5 N 3520 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.550 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.170 Process input model: 60.110 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.048 22351 Z= 0.231 Angle : 0.635 10.477 30397 Z= 0.345 Chirality : 0.042 0.166 3661 Planarity : 0.005 0.080 3770 Dihedral : 12.717 89.887 7626 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.07 (0.15), residues: 2906 helix: 1.12 (0.11), residues: 2165 sheet: -0.18 (0.69), residues: 35 loop : -0.29 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.458 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3824 time to fit residues: 203.2018 Evaluate side-chains 256 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.413 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.0070 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 232 HIS a 499 HIS c 61 ASN ** c 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN d 45 GLN d 182 ASN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 GLN d 303 GLN ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 GLN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 22351 Z= 0.395 Angle : 0.620 9.623 30397 Z= 0.325 Chirality : 0.043 0.184 3661 Planarity : 0.004 0.065 3770 Dihedral : 4.634 38.631 3127 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.15 (0.15), residues: 2906 helix: 1.20 (0.11), residues: 2188 sheet: -0.29 (0.64), residues: 37 loop : -0.38 (0.24), residues: 681 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 24 residues processed: 305 average time/residue: 0.3480 time to fit residues: 164.4556 Evaluate side-chains 284 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 2.622 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2145 time to fit residues: 12.5778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 258 optimal weight: 0.5980 chunk 279 optimal weight: 0.0670 chunk 230 optimal weight: 5.9990 chunk 256 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 499 HIS a 796 HIS c 100 ASN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 GLN ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN k 82 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22351 Z= 0.187 Angle : 0.516 9.812 30397 Z= 0.272 Chirality : 0.038 0.149 3661 Planarity : 0.004 0.059 3770 Dihedral : 4.325 32.585 3127 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.57 (0.15), residues: 2906 helix: 1.50 (0.11), residues: 2198 sheet: -0.11 (0.71), residues: 35 loop : -0.26 (0.25), residues: 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 301 average time/residue: 0.3509 time to fit residues: 162.7300 Evaluate side-chains 268 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1893 time to fit residues: 5.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.8980 chunk 194 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN c 61 ASN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 22351 Z= 0.270 Angle : 0.540 9.451 30397 Z= 0.281 Chirality : 0.039 0.162 3661 Planarity : 0.004 0.058 3770 Dihedral : 4.262 27.709 3127 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.51 (0.15), residues: 2906 helix: 1.46 (0.11), residues: 2210 sheet: -0.22 (0.72), residues: 38 loop : -0.36 (0.24), residues: 658 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 282 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 302 average time/residue: 0.3500 time to fit residues: 163.1374 Evaluate side-chains 279 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 263 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2296 time to fit residues: 9.4763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN a 729 HIS c 61 ASN d 35 GLN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 22351 Z= 0.272 Angle : 0.531 9.838 30397 Z= 0.278 Chirality : 0.039 0.210 3661 Planarity : 0.004 0.057 3770 Dihedral : 4.224 23.394 3127 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.49 (0.15), residues: 2906 helix: 1.46 (0.11), residues: 2209 sheet: -0.12 (0.74), residues: 38 loop : -0.40 (0.24), residues: 659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 2.521 Fit side-chains outliers start: 29 outliers final: 18 residues processed: 304 average time/residue: 0.3604 time to fit residues: 167.6643 Evaluate side-chains 275 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2345 time to fit residues: 10.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 2.9990 chunk 247 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 23 GLN ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN c 132 ASN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 53 ASN ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN m 90 GLN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 22351 Z= 0.377 Angle : 0.590 11.259 30397 Z= 0.305 Chirality : 0.041 0.186 3661 Planarity : 0.004 0.058 3770 Dihedral : 4.322 20.983 3127 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.22 (0.15), residues: 2906 helix: 1.28 (0.11), residues: 2210 sheet: -0.02 (0.75), residues: 35 loop : -0.57 (0.24), residues: 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 275 time to evaluate : 2.629 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 293 average time/residue: 0.3537 time to fit residues: 161.0270 Evaluate side-chains 278 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 260 time to evaluate : 2.502 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2139 time to fit residues: 10.6221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 200 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 231 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 273 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 166 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 384 ASN a 655 HIS c 61 ASN d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22351 Z= 0.203 Angle : 0.521 14.805 30397 Z= 0.270 Chirality : 0.039 0.188 3661 Planarity : 0.003 0.056 3770 Dihedral : 4.155 19.922 3127 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.57 (0.15), residues: 2906 helix: 1.57 (0.11), residues: 2181 sheet: -0.32 (0.76), residues: 38 loop : -0.48 (0.24), residues: 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.737 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 284 average time/residue: 0.3696 time to fit residues: 161.8869 Evaluate side-chains 261 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2196 time to fit residues: 4.3343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 174 optimal weight: 0.0010 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 249 optimal weight: 0.4980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN a 324 ASN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 22351 Z= 0.284 Angle : 0.553 13.419 30397 Z= 0.285 Chirality : 0.040 0.187 3661 Planarity : 0.004 0.055 3770 Dihedral : 4.176 20.052 3127 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.51 (0.15), residues: 2906 helix: 1.52 (0.11), residues: 2180 sheet: -0.26 (0.77), residues: 38 loop : -0.51 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 2.832 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 276 average time/residue: 0.3683 time to fit residues: 158.3280 Evaluate side-chains 271 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 259 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2067 time to fit residues: 7.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 255 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 230 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 chunk 254 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 22351 Z= 0.234 Angle : 0.538 13.608 30397 Z= 0.277 Chirality : 0.039 0.187 3661 Planarity : 0.004 0.056 3770 Dihedral : 4.132 19.998 3127 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.64 (0.15), residues: 2906 helix: 1.63 (0.11), residues: 2170 sheet: -0.30 (0.77), residues: 36 loop : -0.46 (0.23), residues: 700 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 270 time to evaluate : 2.427 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 276 average time/residue: 0.3604 time to fit residues: 154.9102 Evaluate side-chains 267 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 260 time to evaluate : 2.646 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2141 time to fit residues: 6.3735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 282 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 22351 Z= 0.254 Angle : 0.553 14.270 30397 Z= 0.282 Chirality : 0.040 0.209 3661 Planarity : 0.004 0.056 3770 Dihedral : 4.126 19.877 3127 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.55 (0.15), residues: 2906 helix: 1.57 (0.11), residues: 2181 sheet: -0.52 (0.76), residues: 36 loop : -0.50 (0.23), residues: 689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 279 time to evaluate : 2.360 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 284 average time/residue: 0.3860 time to fit residues: 170.7611 Evaluate side-chains 276 residues out of total 2374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 272 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2128 time to fit residues: 4.9948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 209 GLN ** d 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114762 restraints weight = 23533.526| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.58 r_work: 0.3015 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 22351 Z= 0.213 Angle : 0.540 13.778 30397 Z= 0.276 Chirality : 0.039 0.193 3661 Planarity : 0.004 0.060 3770 Dihedral : 4.078 19.668 3127 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.70 (0.15), residues: 2906 helix: 1.68 (0.11), residues: 2168 sheet: -0.61 (0.78), residues: 36 loop : -0.43 (0.23), residues: 702 =============================================================================== Job complete usr+sys time: 4311.02 seconds wall clock time: 79 minutes 30.99 seconds (4770.99 seconds total)