Starting phenix.real_space_refine (version: dev) on Thu Dec 15 08:05:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eas_27984/12_2022/8eas_27984.pdb" } resolution = 2.6 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= 0.007 sd= 0.311 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 ASP 54": "OD1" <-> "OD2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 102": "OD1" <-> "OD2" Residue "a ASP 126": "OD1" <-> "OD2" Residue "a GLU 200": "OE1" <-> "OE2" Residue "a PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 305": "OE1" <-> "OE2" Residue "a TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 108": "OE1" <-> "OE2" Residue "c PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 336": "OE1" <-> "OE2" Residue "e ASP 66": "OD1" <-> "OD2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "i GLU 3": "OE1" <-> "OE2" Residue "i TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 137": "OE1" <-> "OE2" Residue "j ASP 157": "OD1" <-> "OD2" Residue "k GLU 3": "OE1" <-> "OE2" Residue "k TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 137": "OE1" <-> "OE2" Residue "m ASP 157": "OD1" <-> "OD2" Residue "n TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 137": "OE1" <-> "OE2" Residue "n ASP 157": "OD1" <-> "OD2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 24802 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1044 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 995 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'UNK:plan-1': 38, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 919 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "a" Number of atoms: 5948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5948 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 21, 'TRANS': 720} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "b" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 385 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "c" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1473 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "d" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2740 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 565 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "f" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 506 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "g" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "h" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "i" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "j" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1136 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1136 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1129 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "o" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1140 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.69, per 1000 atoms: 0.55 Number of scatterers: 24802 At special positions: 0 Unit cell: (121.54, 162.74, 153.47, 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 146 16.00 O 4465 8.00 N 4005 7.00 C 16186 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: 10.82 Conformation dependent library (CDL) restraints added in 3.8 seconds 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 78.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 15 through 50 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 177 removed outlier: 3.654A pdb=" N ARG A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.994A pdb=" N LYS B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 84 through 107 Processing helix chain 'B' and resid 124 through 151 removed outlier: 3.546A pdb=" N UNK B 132 " --> pdb=" O UNK B 128 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK B 135 " --> pdb=" O UNK B 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.607A pdb=" N ILE F 50 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 102 through 105 Processing helix chain 'F' and resid 106 through 115 removed outlier: 3.529A pdb=" N LYS F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 104 through 146 removed outlier: 3.643A pdb=" N ASP a 108 " --> pdb=" O GLY a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 153 Processing helix chain 'a' and resid 195 through 207 Processing helix chain 'a' and resid 242 through 256 Processing helix chain 'a' and resid 267 through 269 No H-bonds generated for 'chain 'a' and resid 267 through 269' Processing helix chain 'a' and resid 270 through 325 removed outlier: 3.714A pdb=" N THR a 294 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 360 Processing helix chain 'a' and resid 387 through 398 removed outlier: 4.188A pdb=" N TYR a 397 " --> pdb=" O ILE a 393 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY a 398 " --> pdb=" O CYS a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 423 removed outlier: 4.444A 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 442 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 480 Processing helix chain 'a' and resid 519 through 523 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.665A pdb=" N SER a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 571 Processing helix chain 'a' and resid 571 through 596 removed outlier: 3.807A pdb=" N GLY a 575 " --> pdb=" O ASN a 571 " (cutoff:3.500A) removed outlier: 4.837A 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: 3.734A pdb=" N PHE a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 629 through 658 removed outlier: 3.704A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 4.706A 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 710 through 733 removed outlier: 3.801A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR a 730 " --> pdb=" O CYS a 726 " (cutoff:3.500A) Processing helix chain 'a' and resid 733 through 753 removed outlier: 4.373A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 759 removed outlier: 3.558A pdb=" N ALA a 758 " --> pdb=" O THR a 754 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE a 759 " --> pdb=" O ILE a 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 754 through 759' Processing helix chain 'a' and resid 762 through 785 Processing helix chain 'a' and resid 787 through 803 Processing helix chain 'a' and resid 805 through 810 removed outlier: 3.997A pdb=" N PHE a 809 " --> pdb=" O SER a 805 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 833 Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'c' and resid 17 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: 3.645A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 95 No H-bonds generated for 'chain 'c' and resid 93 through 95' Processing helix chain 'c' and resid 96 through 123 removed outlier: 4.818A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 133 removed outlier: 3.553A pdb=" N MET c 133 " --> pdb=" O ALA c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 180 through 206 removed outlier: 3.880A pdb=" N ILE c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 6 removed outlier: 3.576A pdb=" N PHE d 6 " --> pdb=" O GLU d 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 2 through 6' Processing helix chain 'd' and resid 6 through 23 removed outlier: 3.548A pdb=" N GLY d 11 " --> pdb=" O ASN d 7 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE d 12 " --> pdb=" O ILE d 8 " (cutoff:3.500A) removed outlier: 5.136A 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 47 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 88 through 116 removed outlier: 3.942A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 126 Processing helix chain 'd' and resid 136 through 141 removed outlier: 3.510A pdb=" N SER d 140 " --> pdb=" O PRO d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 152 Processing helix chain 'd' and resid 158 through 163 removed outlier: 3.734A pdb=" N LYS d 163 " --> pdb=" O PRO d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 Processing helix chain 'd' and resid 201 through 228 removed outlier: 3.755A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.542A pdb=" N SER d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 257 Processing helix chain 'd' and resid 261 through 270 Processing helix chain 'd' and resid 283 through 300 Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.184A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 25 removed outlier: 3.907A pdb=" N VAL e 7 " --> pdb=" O SER e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 55 removed outlier: 3.638A pdb=" N GLN e 55 " --> pdb=" O THR e 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 33 Processing helix chain 'f' and resid 35 through 40 Processing helix chain 'f' and resid 48 through 76 Processing helix chain 'g' and resid 8 through 46 removed outlier: 4.045A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 54 Processing helix chain 'g' and resid 54 through 77 removed outlier: 4.027A pdb=" N ILE g 63 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 122 Processing helix chain 'g' and resid 124 through 154 removed outlier: 4.171A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 43 removed outlier: 4.007A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (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 Processing helix chain 'h' and resid 54 through 76 Processing helix chain 'h' and resid 83 through 122 removed outlier: 3.997A pdb=" N GLN h 121 " --> pdb=" O ARG h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 153 removed outlier: 4.324A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 46 removed outlier: 4.001A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU i 45 " --> pdb=" O ALA i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 76 Processing helix chain 'i' and resid 83 through 122 removed outlier: 3.785A pdb=" N GLN i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 153 removed outlier: 4.376A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 43 removed outlier: 4.058A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (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 77 Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 124 through 155 removed outlier: 4.249A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.118A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) 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 77 Processing helix chain 'k' and resid 83 through 122 Processing helix chain 'k' and resid 124 through 152 removed outlier: 4.424A pdb=" N GLY k 128 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 43 removed outlier: 4.161A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 48 No H-bonds generated for 'chain 'l' and resid 46 through 48' Processing helix chain 'l' and resid 49 through 54 Processing helix chain 'l' and resid 54 through 77 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.648A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.189A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 43 removed outlier: 4.089A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 45 No H-bonds generated for 'chain 'm' and resid 44 through 45' Processing helix chain 'm' and resid 46 through 50 Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 83 through 120 Processing helix chain 'm' and resid 124 through 155 removed outlier: 4.194A pdb=" N GLY m 128 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR m 155 " --> pdb=" O ASN m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 44 removed outlier: 4.142A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 46 through 48 No H-bonds generated for 'chain 'n' and resid 46 through 48' Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 54 through 78 Processing helix chain 'n' and resid 83 through 122 removed outlier: 3.740A pdb=" N GLN n 121 " --> pdb=" O ARG n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 153 removed outlier: 4.330A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 49 removed outlier: 3.921A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 84 removed outlier: 3.660A pdb=" N ASN o 83 " --> pdb=" O LEU o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 130 removed outlier: 4.768A pdb=" N ARG o 125 " --> pdb=" O ASP o 121 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS o 126 " --> pdb=" O VAL o 122 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN o 130 " --> pdb=" O LYS o 126 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 164 removed outlier: 4.085A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 removed outlier: 4.018A pdb=" N GLU B 70 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 37 through 39 removed outlier: 8.131A pdb=" N PHE F 38 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL F 10 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU F 7 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA F 65 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU F 92 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 67 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE F 94 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA5, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'a' and resid 213 through 217 removed outlier: 4.332A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 222 through 224 Processing sheet with id=AA8, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA9, first strand: chain 'a' and resid 506 through 507 1980 hydrogen bonds defined for protein. 5847 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: 9.04 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6924 1.33 - 1.45: 4128 1.45 - 1.57: 14012 1.57 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 25284 Sorted by residual: bond pdb=" CB GLU i 137 " pdb=" CG GLU i 137 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.38e+00 bond pdb=" CB GLU k 137 " pdb=" CG GLU k 137 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" CB TRP c 77 " pdb=" CG TRP c 77 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.50e+00 bond pdb=" CB VAL c 110 " pdb=" CG1 VAL c 110 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" C ASN d 333 " pdb=" O ASN d 333 " ideal model delta sigma weight residual 1.243 1.229 0.015 9.50e-03 1.11e+04 2.44e+00 ... (remaining 25279 not shown) Histogram of bond angle deviations from ideal: 96.52 - 104.04: 270 104.04 - 111.55: 11710 111.55 - 119.07: 8703 119.07 - 126.58: 13405 126.58 - 134.10: 235 Bond angle restraints: 34323 Sorted by residual: angle pdb=" CB MET i 59 " pdb=" CG MET i 59 " pdb=" SD MET i 59 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C ILE c 79 " pdb=" N PHE c 80 " pdb=" CA PHE c 80 " ideal model delta sigma weight residual 120.31 114.35 5.96 1.52e+00 4.33e-01 1.54e+01 angle pdb=" C TRP c 77 " pdb=" CA TRP c 77 " pdb=" CB TRP c 77 " ideal model delta sigma weight residual 110.96 105.57 5.39 1.54e+00 4.22e-01 1.22e+01 angle pdb=" C PHE a 483 " pdb=" N SER a 484 " pdb=" CA SER a 484 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C ASN d 333 " pdb=" CA ASN d 333 " pdb=" CB ASN d 333 " ideal model delta sigma weight residual 117.23 112.85 4.38 1.36e+00 5.41e-01 1.04e+01 ... (remaining 34318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13638 17.66 - 35.31: 961 35.31 - 52.97: 132 52.97 - 70.62: 33 70.62 - 88.28: 23 Dihedral angle restraints: 14787 sinusoidal: 5439 harmonic: 9348 Sorted by residual: dihedral pdb=" CA ASN A 49 " pdb=" C ASN A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PRO d 201 " pdb=" C PRO d 201 " pdb=" N GLU d 202 " pdb=" CA GLU d 202 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA THR a 754 " pdb=" C THR a 754 " pdb=" N ILE a 755 " pdb=" CA ILE a 755 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 14784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2544 0.037 - 0.073: 1186 0.073 - 0.110: 294 0.110 - 0.146: 43 0.146 - 0.183: 9 Chirality restraints: 4076 Sorted by residual: chirality pdb=" CA TRP c 77 " pdb=" N TRP c 77 " pdb=" C TRP c 77 " pdb=" CB TRP c 77 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CG LEU k 144 " pdb=" CB LEU k 144 " pdb=" CD1 LEU k 144 " pdb=" CD2 LEU k 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CG LEU n 144 " pdb=" CB LEU n 144 " pdb=" CD1 LEU n 144 " pdb=" CD2 LEU n 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 4073 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " -0.041 2.00e-02 2.50e+03 4.66e-02 5.42e+01 pdb=" CG TRP c 77 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR a 627 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO a 628 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO a 628 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO a 628 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU k 137 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" CD GLU k 137 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU k 137 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU k 137 " -0.011 2.00e-02 2.50e+03 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 211 2.62 - 3.19: 23283 3.19 - 3.76: 43055 3.76 - 4.33: 60337 4.33 - 4.90: 97687 Nonbonded interactions: 224573 Sorted by model distance: nonbonded pdb=" OD1 ASP d 105 " pdb=" OH TYR d 185 " model vdw 2.044 2.440 nonbonded pdb=" OG SER A 25 " pdb=" OE1 GLN B 43 " model vdw 2.053 2.440 nonbonded pdb=" O LEU g 78 " pdb=" NH2 ARG h 153 " model vdw 2.145 2.520 nonbonded pdb=" OH TYR a 73 " pdb=" OE2 GLU a 828 " model vdw 2.162 2.440 nonbonded pdb=" NH2 ARG d 18 " pdb=" O PHE d 300 " model vdw 2.166 2.520 ... (remaining 224568 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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'h' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'i' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'j' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 159)) selection = (chain 'k' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 49 or (resid 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 through 159)) selection = (chain 'l' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 49 or (resid 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 through 159)) selection = (chain 'm' and (resid 2 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 159)) selection = (chain 'n' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) } 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 146 5.16 5 C 16186 2.51 5 N 4005 2.21 5 O 4465 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.980 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.180 Process input model: 65.050 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.110 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:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 0.082 25284 Z= 0.375 Angle : 0.639 13.372 34323 Z= 0.343 Chirality : 0.043 0.183 4076 Planarity : 0.004 0.065 4288 Dihedral : 12.905 88.277 8831 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.65 (0.14), residues: 3193 helix: 1.57 (0.10), residues: 2324 sheet: 0.59 (0.63), residues: 68 loop : -0.13 (0.20), residues: 801 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.2746 time to fit residues: 575.5774 Evaluate side-chains 316 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 276 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: ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 156 GLN l 151 ASN n 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 25284 Z= 0.241 Angle : 0.520 7.782 34323 Z= 0.276 Chirality : 0.039 0.149 4076 Planarity : 0.004 0.037 4288 Dihedral : 4.294 32.015 3503 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.89 (0.14), residues: 3193 helix: 1.78 (0.10), residues: 2343 sheet: 0.50 (0.65), residues: 66 loop : -0.19 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 343 time to evaluate : 3.042 Fit side-chains outliers start: 40 outliers final: 14 residues processed: 358 average time/residue: 1.2693 time to fit residues: 530.7800 Evaluate side-chains 331 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 317 time to evaluate : 2.806 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 5 residues processed: 9 average time/residue: 0.2764 time to fit residues: 8.4049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 chunk 246 optimal weight: 0.6980 chunk 274 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 25284 Z= 0.177 Angle : 0.470 9.316 34323 Z= 0.251 Chirality : 0.037 0.168 4076 Planarity : 0.003 0.036 4288 Dihedral : 4.087 34.348 3503 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.20 (0.14), residues: 3193 helix: 2.03 (0.10), residues: 2342 sheet: 0.40 (0.61), residues: 73 loop : -0.13 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 339 time to evaluate : 3.017 Fit side-chains outliers start: 38 outliers final: 16 residues processed: 357 average time/residue: 1.2536 time to fit residues: 526.1823 Evaluate side-chains 334 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 318 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.2486 time to fit residues: 5.9717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9980 chunk 207 optimal weight: 0.2980 chunk 143 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 263 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 25284 Z= 0.177 Angle : 0.468 11.560 34323 Z= 0.248 Chirality : 0.037 0.150 4076 Planarity : 0.003 0.037 4288 Dihedral : 4.023 34.300 3503 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.30 (0.14), residues: 3193 helix: 2.10 (0.10), residues: 2348 sheet: 0.37 (0.61), residues: 73 loop : -0.12 (0.21), residues: 772 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 331 time to evaluate : 3.181 Fit side-chains outliers start: 44 outliers final: 23 residues processed: 354 average time/residue: 1.2306 time to fit residues: 512.2338 Evaluate side-chains 343 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 14 residues processed: 9 average time/residue: 0.2558 time to fit residues: 8.1051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 250 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 263 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 25284 Z= 0.364 Angle : 0.560 7.637 34323 Z= 0.295 Chirality : 0.041 0.175 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.323 36.547 3503 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.86 (0.14), residues: 3193 helix: 1.75 (0.10), residues: 2347 sheet: 0.32 (0.64), residues: 65 loop : -0.17 (0.20), residues: 781 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 327 time to evaluate : 3.101 Fit side-chains outliers start: 59 outliers final: 32 residues processed: 357 average time/residue: 1.2443 time to fit residues: 523.6134 Evaluate side-chains 346 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 18 residues processed: 14 average time/residue: 0.3237 time to fit residues: 11.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0000 chunk 264 optimal weight: 0.0670 chunk 58 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 294 optimal weight: 0.4980 chunk 244 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN f 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 25284 Z= 0.146 Angle : 0.457 7.176 34323 Z= 0.245 Chirality : 0.037 0.148 4076 Planarity : 0.003 0.038 4288 Dihedral : 4.008 38.923 3503 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.33 (0.15), residues: 3193 helix: 2.15 (0.10), residues: 2340 sheet: 0.38 (0.57), residues: 82 loop : -0.18 (0.21), residues: 771 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 336 time to evaluate : 3.029 Fit side-chains outliers start: 44 outliers final: 18 residues processed: 366 average time/residue: 1.1554 time to fit residues: 500.7243 Evaluate side-chains 334 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 316 time to evaluate : 3.039 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.2160 time to fit residues: 5.8602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 293 optimal weight: 0.0370 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 25284 Z= 0.184 Angle : 0.475 7.923 34323 Z= 0.251 Chirality : 0.037 0.143 4076 Planarity : 0.003 0.040 4288 Dihedral : 3.983 37.226 3503 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.37 (0.14), residues: 3193 helix: 2.17 (0.10), residues: 2349 sheet: 0.43 (0.57), residues: 82 loop : -0.14 (0.21), residues: 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 321 time to evaluate : 3.208 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 344 average time/residue: 1.2631 time to fit residues: 513.4813 Evaluate side-chains 326 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 305 time to evaluate : 2.900 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.2545 time to fit residues: 6.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 199 optimal weight: 0.4980 chunk 144 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN f 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25284 Z= 0.220 Angle : 0.499 10.392 34323 Z= 0.262 Chirality : 0.038 0.154 4076 Planarity : 0.004 0.046 4288 Dihedral : 4.046 37.705 3503 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.29 (0.14), residues: 3193 helix: 2.09 (0.10), residues: 2350 sheet: 0.45 (0.57), residues: 82 loop : -0.13 (0.21), residues: 761 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 317 time to evaluate : 2.920 Fit side-chains outliers start: 39 outliers final: 25 residues processed: 344 average time/residue: 1.2364 time to fit residues: 500.1227 Evaluate side-chains 340 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 315 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.2467 time to fit residues: 7.3687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 25284 Z= 0.226 Angle : 0.506 10.253 34323 Z= 0.266 Chirality : 0.038 0.150 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.074 38.683 3503 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.25 (0.14), residues: 3193 helix: 2.05 (0.10), residues: 2349 sheet: 0.56 (0.59), residues: 76 loop : -0.13 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 321 time to evaluate : 2.686 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 345 average time/residue: 1.2355 time to fit residues: 505.4147 Evaluate side-chains 337 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 2.862 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.3199 time to fit residues: 6.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 2.9990 chunk 288 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 302 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 186 optimal weight: 0.5980 chunk 147 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25284 Z= 0.194 Angle : 0.493 8.388 34323 Z= 0.260 Chirality : 0.038 0.145 4076 Planarity : 0.004 0.043 4288 Dihedral : 4.023 39.030 3503 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.32 (0.14), residues: 3193 helix: 2.12 (0.10), residues: 2344 sheet: 0.48 (0.58), residues: 82 loop : -0.13 (0.21), residues: 767 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 318 time to evaluate : 2.606 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 340 average time/residue: 1.2433 time to fit residues: 498.6939 Evaluate side-chains 327 residues out of total 2652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 3.018 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 3.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105174 restraints weight = 25239.381| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.36 r_work: 0.3108 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 25284 Z= 0.211 Angle : 0.499 9.910 34323 Z= 0.263 Chirality : 0.038 0.146 4076 Planarity : 0.004 0.046 4288 Dihedral : 4.036 38.980 3503 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.29 (0.14), residues: 3193 helix: 2.09 (0.10), residues: 2349 sheet: 0.50 (0.58), residues: 82 loop : -0.14 (0.21), residues: 762 =============================================================================== Job complete usr+sys time: 8608.68 seconds wall clock time: 155 minutes 4.41 seconds (9304.41 seconds total)