Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 13 15:57:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoi_28376/07_2023/8eoi_28376_updated.pdb" } resolution = 3.4 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 18562 2.51 5 N 4861 2.21 5 O 5159 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 239": "OD1" <-> "OD2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 28721 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7444 Classifications: {'peptide': 936} Link IDs: {'PCIS': 3, 'PTRANS': 40, 'TRANS': 892} Chain breaks: 2 Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2403 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain: "C" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1777 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain breaks: 2 Chain: "E" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 806 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 929 Classifications: {'peptide': 116} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Chain: "H" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "I" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1150 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "K" Number of atoms: 9024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 9024 Classifications: {'peptide': 1116} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1077} Chain breaks: 6 Chain: "J" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2364 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 363 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain breaks: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.75, per 1000 atoms: 0.44 Number of scatterers: 28721 At special positions: 0 Unit cell: (115.138, 163.394, 233.662, 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 139 16.00 O 5159 8.00 N 4861 7.00 C 18562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS K 316 " - pdb=" SG CYS K 332 " distance=2.03 Simple disulfide: pdb=" SG CYS K1479 " - pdb=" SG CYS K1495 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1001 " - " ASN A 370 " " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN I 182 " Time building additional restraints: 10.55 Conformation dependent library (CDL) restraints added in 3.7 seconds 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 25 sheets defined 42.1% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 447 through 450 removed outlier: 3.790A pdb=" N ALA A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 480 through 505 removed outlier: 4.600A pdb=" N PHE A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N MET A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 656 through 668 Proline residue: A 667 - end of helix Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 906 through 908 No H-bonds generated for 'chain 'A' and resid 906 through 908' Processing helix chain 'A' and resid 962 through 991 Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.722A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.568A pdb=" N MET B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.661A pdb=" N GLN B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.687A pdb=" N THR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 205 through 221 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 247 through 274 removed outlier: 3.730A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 removed outlier: 4.000A pdb=" N VAL B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 37 removed outlier: 3.890A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Proline residue: C 19 - end of helix Processing helix chain 'C' and resid 46 through 67 removed outlier: 6.185A pdb=" N LYS C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 115 through 132 Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 146 through 152 Proline residue: C 150 - end of helix No H-bonds generated for 'chain 'C' and resid 146 through 152' Processing helix chain 'C' and resid 168 through 186 removed outlier: 3.916A pdb=" N LEU C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILE C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 removed outlier: 4.228A pdb=" N LEU C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'E' and resid 5 through 34 removed outlier: 3.546A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 62 removed outlier: 3.769A pdb=" N HIS E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 84 No H-bonds generated for 'chain 'E' and resid 81 through 84' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 96 through 100 Processing helix chain 'F' and resid 16 through 44 Processing helix chain 'F' and resid 49 through 70 removed outlier: 3.638A pdb=" N PHE F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 82 through 85 No H-bonds generated for 'chain 'F' and resid 82 through 85' Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 8 through 20 Processing helix chain 'H' and resid 68 through 84 Processing helix chain 'H' and resid 106 through 118 removed outlier: 3.545A pdb=" N GLU H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 176 Processing helix chain 'H' and resid 179 through 181 No H-bonds generated for 'chain 'H' and resid 179 through 181' Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 200 through 208 Processing helix chain 'I' and resid 92 through 103 Processing helix chain 'I' and resid 135 through 138 No H-bonds generated for 'chain 'I' and resid 135 through 138' Processing helix chain 'I' and resid 175 through 177 No H-bonds generated for 'chain 'I' and resid 175 through 177' Processing helix chain 'I' and resid 199 through 205 Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'K' and resid 124 through 143 removed outlier: 3.830A pdb=" N ILE K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 181 removed outlier: 3.542A pdb=" N ARG K 161 " --> pdb=" O SER K 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 210 Processing helix chain 'K' and resid 236 through 249 Proline residue: K 244 - end of helix Processing helix chain 'K' and resid 255 through 266 removed outlier: 3.513A pdb=" N MET K 265 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 266 " --> pdb=" O ILE K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 289 removed outlier: 3.528A pdb=" N LEU K 274 " --> pdb=" O HIS K 270 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL K 275 " --> pdb=" O ILE K 271 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU K 276 " --> pdb=" O ALA K 272 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA K 283 " --> pdb=" O ILE K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 360 Processing helix chain 'K' and resid 365 through 376 Processing helix chain 'K' and resid 382 through 411 removed outlier: 4.015A pdb=" N LYS K 410 " --> pdb=" O GLY K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 446 Processing helix chain 'K' and resid 508 through 521 removed outlier: 3.627A pdb=" N LYS K 516 " --> pdb=" O PHE K 512 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 521 " --> pdb=" O CYS K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 524 through 541 Processing helix chain 'K' and resid 553 through 566 removed outlier: 3.775A pdb=" N THR K 558 " --> pdb=" O GLU K 554 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA K 559 " --> pdb=" O VAL K 555 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN K 560 " --> pdb=" O GLN K 556 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS K 561 " --> pdb=" O ASP K 557 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA K 565 " --> pdb=" O LYS K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 576 Processing helix chain 'K' and resid 580 through 583 No H-bonds generated for 'chain 'K' and resid 580 through 583' Processing helix chain 'K' and resid 589 through 606 Processing helix chain 'K' and resid 615 through 632 removed outlier: 3.912A pdb=" N ILE K 627 " --> pdb=" O ARG K 623 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE K 628 " --> pdb=" O LEU K 624 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS K 629 " --> pdb=" O LEU K 625 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE K 630 " --> pdb=" O ARG K 626 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 673 removed outlier: 3.624A pdb=" N VAL K 648 " --> pdb=" O LEU K 644 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG K 649 " --> pdb=" O LEU K 645 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER K 650 " --> pdb=" O ASN K 646 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER K 653 " --> pdb=" O ARG K 649 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU K 654 " --> pdb=" O SER K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 692 through 704 Processing helix chain 'K' and resid 708 through 718 Processing helix chain 'K' and resid 725 through 758 removed outlier: 3.726A pdb=" N LEU K 728 " --> pdb=" O PRO K 725 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL K 729 " --> pdb=" O GLY K 726 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE K 731 " --> pdb=" O LEU K 728 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE K 735 " --> pdb=" O TYR K 732 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N CYS K 739 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR K 742 " --> pdb=" O CYS K 739 " (cutoff:3.500A) Processing helix chain 'K' and resid 1024 through 1028 Processing helix chain 'K' and resid 1036 through 1070 removed outlier: 5.060A pdb=" N ARG K1047 " --> pdb=" O PHE K1043 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR K1048 " --> pdb=" O VAL K1044 " (cutoff:3.500A) Processing helix chain 'K' and resid 1124 through 1131 removed outlier: 3.891A pdb=" N VAL K1131 " --> pdb=" O ALA K1127 " (cutoff:3.500A) Processing helix chain 'K' and resid 1137 through 1144 Processing helix chain 'K' and resid 1160 through 1191 removed outlier: 4.614A pdb=" N TYR K1169 " --> pdb=" O PHE K1166 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET K1177 " --> pdb=" O ALA K1174 " (cutoff:3.500A) Processing helix chain 'K' and resid 1206 through 1213 Processing helix chain 'K' and resid 1228 through 1235 Processing helix chain 'K' and resid 1239 through 1256 Processing helix chain 'K' and resid 1265 through 1290 Processing helix chain 'K' and resid 1295 through 1326 No H-bonds generated for 'chain 'K' and resid 1295 through 1326' Processing helix chain 'K' and resid 1330 through 1346 Processing helix chain 'K' and resid 1375 through 1390 removed outlier: 3.521A pdb=" N LEU K1384 " --> pdb=" O ARG K1380 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL K1385 " --> pdb=" O VAL K1381 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU K1387 " --> pdb=" O ARG K1383 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU K1388 " --> pdb=" O LEU K1384 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER K1389 " --> pdb=" O VAL K1385 " (cutoff:3.500A) Processing helix chain 'K' and resid 1392 through 1404 removed outlier: 4.973A pdb=" N LEU K1397 " --> pdb=" O GLY K1393 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS K1403 " --> pdb=" O TRP K1399 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER K1404 " --> pdb=" O THR K1400 " (cutoff:3.500A) Processing helix chain 'K' and resid 1408 through 1429 removed outlier: 3.624A pdb=" N ILE K1425 " --> pdb=" O ILE K1421 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY K1426 " --> pdb=" O TYR K1422 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET K1427 " --> pdb=" O ALA K1423 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN K1428 " --> pdb=" O VAL K1424 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL K1429 " --> pdb=" O ILE K1425 " (cutoff:3.500A) Processing helix chain 'K' and resid 1450 through 1461 Processing helix chain 'K' and resid 1466 through 1472 Processing helix chain 'K' and resid 1500 through 1525 Processing helix chain 'K' and resid 1539 through 1552 Processing helix chain 'K' and resid 1562 through 1565 No H-bonds generated for 'chain 'K' and resid 1562 through 1565' Processing helix chain 'K' and resid 1587 through 1592 Processing helix chain 'K' and resid 1606 through 1617 Processing helix chain 'K' and resid 1626 through 1634 Processing helix chain 'K' and resid 1647 through 1652 Processing helix chain 'J' and resid 39 through 54 Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 191 through 207 removed outlier: 3.549A pdb=" N LEU J 200 " --> pdb=" O MET J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 263 removed outlier: 3.593A pdb=" N SER J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 280 Processing helix chain 'J' and resid 297 through 307 Processing helix chain 'J' and resid 315 through 326 Processing helix chain 'J' and resid 330 through 332 No H-bonds generated for 'chain 'J' and resid 330 through 332' Processing helix chain 'J' and resid 342 through 359 removed outlier: 3.545A pdb=" N TYR J 352 " --> pdb=" O HIS J 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'A' and resid 40 through 44 removed outlier: 7.046A pdb=" N ALA A 57 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 43 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 55 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP A 75 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 119 through 122 removed outlier: 3.634A pdb=" N TRP A 119 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 134 removed outlier: 7.050A pdb=" N LEU A 146 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 131 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA A 144 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 133 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR A 142 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 174 through 180 removed outlier: 6.926A pdb=" N LEU A 189 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 178 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N TRP A 187 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER A 180 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N VAL A 185 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 228 through 230 Processing sheet with id= G, first strand: chain 'A' and resid 275 through 277 removed outlier: 6.880A pdb=" N HIS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN A 304 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU A 312 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 306 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU A 310 " --> pdb=" O HIS A 306 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 321 through 327 Processing sheet with id= I, first strand: chain 'A' and resid 404 through 411 removed outlier: 3.542A pdb=" N ARG A 404 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 443 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 452 through 459 removed outlier: 6.847A pdb=" N VAL A 539 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU A 455 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 537 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N MET A 457 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET A 535 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 599 through 604 removed outlier: 6.811A pdb=" N THR A 588 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL A 574 " --> pdb=" O THR A 588 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU A 572 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LYS A 592 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 570 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 649 through 652 Processing sheet with id= M, first strand: chain 'A' and resid 670 through 675 removed outlier: 5.942A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 723 through 725 Processing sheet with id= O, first strand: chain 'A' and resid 705 through 711 removed outlier: 6.877A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 756 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP A 763 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 769 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 783 through 787 removed outlier: 3.610A pdb=" N HIS A 783 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN A 803 " --> pdb=" O PHE A 840 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 846 through 849 Processing sheet with id= R, first strand: chain 'G' and resid 84 through 86 removed outlier: 6.232A pdb=" N LEU G 138 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL G 52 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET G 140 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 74 through 76 Processing sheet with id= T, first strand: chain 'H' and resid 150 through 153 removed outlier: 6.724A pdb=" N LEU H 30 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR H 92 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY H 28 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN H 94 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL H 26 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU H 29 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL H 31 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N CYS H 57 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 127 through 133 removed outlier: 6.672A pdb=" N LEU I 55 " --> pdb=" O PRO I 113 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS I 58 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS I 70 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 182 through 188 Processing sheet with id= W, first strand: chain 'J' and resid 115 through 118 removed outlier: 3.829A pdb=" N GLU J 97 " --> pdb=" O ILE J 105 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG J 107 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE J 95 " --> pdb=" O ARG J 107 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR J 66 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE J 92 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL J 64 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS J 94 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE J 62 " --> pdb=" O HIS J 94 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 180 through 183 removed outlier: 5.965A pdb=" N ILE J 288 " --> pdb=" O VAL J 181 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL J 183 " --> pdb=" O ILE J 288 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL J 290 " --> pdb=" O VAL J 183 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J 335 " --> pdb=" O PHE J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 212 through 217 removed outlier: 6.603A pdb=" N LEU J 266 " --> pdb=" O SER J 213 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR J 215 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL J 268 " --> pdb=" O THR J 215 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL J 217 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP J 270 " --> pdb=" O VAL J 217 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 1272 hydrogen bonds defined for protein. 3522 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: 9.78 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9179 1.34 - 1.46: 6822 1.46 - 1.58: 13156 1.58 - 1.70: 1 1.70 - 1.82: 223 Bond restraints: 29381 Sorted by residual: bond pdb=" C73 9Z9 K1701 " pdb=" O80 9Z9 K1701 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" C48 9Z9 K1701 " pdb=" O49 9Z9 K1701 " ideal model delta sigma weight residual 1.402 1.444 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C24 9Z9 K1701 " pdb=" O25 9Z9 K1701 " ideal model delta sigma weight residual 1.403 1.441 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C06 9Z9 K1701 " pdb=" C07 9Z9 K1701 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 29376 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 620 105.87 - 112.91: 15887 112.91 - 119.95: 9912 119.95 - 126.99: 13045 126.99 - 134.03: 363 Bond angle restraints: 39827 Sorted by residual: angle pdb=" N VAL H 137 " pdb=" CA VAL H 137 " pdb=" C VAL H 137 " ideal model delta sigma weight residual 113.71 108.17 5.54 9.50e-01 1.11e+00 3.40e+01 angle pdb=" N ILE K1373 " pdb=" CA ILE K1373 " pdb=" C ILE K1373 " ideal model delta sigma weight residual 113.20 108.02 5.18 9.60e-01 1.09e+00 2.91e+01 angle pdb=" N VAL H 4 " pdb=" CA VAL H 4 " pdb=" C VAL H 4 " ideal model delta sigma weight residual 113.53 108.84 4.69 9.80e-01 1.04e+00 2.30e+01 angle pdb=" C LYS C 254 " pdb=" CA LYS C 254 " pdb=" CB LYS C 254 " ideal model delta sigma weight residual 115.79 111.42 4.37 1.19e+00 7.06e-01 1.35e+01 angle pdb=" C LYS D 50 " pdb=" N GLN D 51 " pdb=" CA GLN D 51 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 ... (remaining 39822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 16678 21.85 - 43.70: 667 43.70 - 65.54: 83 65.54 - 87.39: 18 87.39 - 109.24: 3 Dihedral angle restraints: 17449 sinusoidal: 7058 harmonic: 10391 Sorted by residual: dihedral pdb=" CA ASP D 49 " pdb=" C ASP D 49 " pdb=" N LYS D 50 " pdb=" CA LYS D 50 " ideal model delta harmonic sigma weight residual 180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C73 9Z9 K1701 " pdb=" C76 9Z9 K1701 " pdb=" C77 9Z9 K1701 " pdb=" C78 9Z9 K1701 " ideal model delta sinusoidal sigma weight residual 51.88 -57.36 109.24 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C23 9Z9 K1701 " pdb=" C21 9Z9 K1701 " pdb=" C22 9Z9 K1701 " pdb=" O20 9Z9 K1701 " ideal model delta sinusoidal sigma weight residual 177.26 -73.77 -108.97 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 17446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3500 0.045 - 0.090: 777 0.090 - 0.135: 225 0.135 - 0.179: 9 0.179 - 0.224: 3 Chirality restraints: 4514 Sorted by residual: chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 370 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C17 9Z9 K1701 " pdb=" C16 9Z9 K1701 " pdb=" C18 9Z9 K1701 " pdb=" O20 9Z9 K1701 " both_signs ideal model delta sigma weight residual False 2.46 2.68 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C73 9Z9 K1701 " pdb=" C76 9Z9 K1701 " pdb=" O72 9Z9 K1701 " pdb=" O80 9Z9 K1701 " both_signs ideal model delta sigma weight residual False 2.26 2.48 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 4511 not shown) Planarity restraints: 5014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K1573 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO K1574 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO K1574 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO K1574 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K1654 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO K1655 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO K1655 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K1655 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 132 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.85e+00 pdb=" N PRO I 133 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 133 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 133 " 0.027 5.00e-02 4.00e+02 ... (remaining 5011 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 579 2.69 - 3.24: 28295 3.24 - 3.79: 43975 3.79 - 4.35: 56108 4.35 - 4.90: 92953 Nonbonded interactions: 221910 Sorted by model distance: nonbonded pdb=" O PRO C 141 " pdb=" OG1 THR F 47 " model vdw 2.137 2.440 nonbonded pdb=" O ALA K1127 " pdb=" OG1 THR K1130 " model vdw 2.166 2.440 nonbonded pdb=" O ARG K1370 " pdb=" OG1 THR K1374 " model vdw 2.168 2.440 nonbonded pdb=" O LEU K1613 " pdb=" OG1 THR K1616 " model vdw 2.218 2.440 nonbonded pdb=" O ILE K 751 " pdb=" N ASN K 755 " model vdw 2.227 2.520 ... (remaining 221905 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 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.390 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: 20.850 Check model and map are aligned: 0.490 Set scattering table: 0.210 Process input model: 65.160 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.120 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.002 0.045 29381 Z= 0.153 Angle : 0.506 7.997 39827 Z= 0.269 Chirality : 0.040 0.224 4514 Planarity : 0.004 0.050 5010 Dihedral : 11.589 109.238 10711 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.36 % Favored : 94.62 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3510 helix: 1.62 (0.14), residues: 1515 sheet: 0.58 (0.23), residues: 557 loop : -1.75 (0.16), residues: 1438 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 152 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 34 residues processed: 232 average time/residue: 0.3695 time to fit residues: 142.8546 Evaluate side-chains 165 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 3.274 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2917 time to fit residues: 21.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.0670 chunk 266 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 319 optimal weight: 50.0000 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 273 GLN A 280 GLN A 705 GLN A 952 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN E 19 HIS E 48 GLN H 158 HIS H 199 ASN I 188 GLN K 325 GLN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 GLN K 443 GLN K 581 GLN K 671 GLN K 701 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1206 GLN K1259 GLN ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN K1595 ASN K1599 ASN J 47 GLN J 50 GLN J 251 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29381 Z= 0.170 Angle : 0.524 8.946 39827 Z= 0.266 Chirality : 0.041 0.294 4514 Planarity : 0.003 0.050 5010 Dihedral : 4.883 108.160 3876 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.15), residues: 3510 helix: 1.73 (0.14), residues: 1517 sheet: 0.54 (0.23), residues: 560 loop : -1.70 (0.16), residues: 1433 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 17 residues processed: 170 average time/residue: 0.3729 time to fit residues: 108.1611 Evaluate side-chains 149 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2762 time to fit residues: 13.2057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 345 optimal weight: 0.0770 chunk 285 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29381 Z= 0.206 Angle : 0.527 8.973 39827 Z= 0.269 Chirality : 0.041 0.298 4514 Planarity : 0.003 0.050 5010 Dihedral : 4.872 108.565 3876 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3510 helix: 1.71 (0.14), residues: 1525 sheet: 0.51 (0.23), residues: 560 loop : -1.70 (0.16), residues: 1425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 18 residues processed: 172 average time/residue: 0.3735 time to fit residues: 108.7224 Evaluate side-chains 149 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 3.478 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2574 time to fit residues: 13.5281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.0670 chunk 240 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 321 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 304 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 550 ASN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29381 Z= 0.170 Angle : 0.518 9.121 39827 Z= 0.264 Chirality : 0.040 0.299 4514 Planarity : 0.003 0.050 5010 Dihedral : 4.806 108.766 3876 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3510 helix: 1.71 (0.14), residues: 1529 sheet: 0.56 (0.23), residues: 561 loop : -1.67 (0.16), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 160 average time/residue: 0.4116 time to fit residues: 111.9365 Evaluate side-chains 144 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 3.645 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3024 time to fit residues: 13.1038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 253 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 290 optimal weight: 30.0000 chunk 235 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS K 443 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 29381 Z= 0.423 Angle : 0.629 14.116 39827 Z= 0.323 Chirality : 0.044 0.310 4514 Planarity : 0.004 0.049 5010 Dihedral : 5.076 109.576 3876 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.07 % Favored : 92.91 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3510 helix: 1.58 (0.14), residues: 1526 sheet: 0.39 (0.22), residues: 548 loop : -1.79 (0.16), residues: 1436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 128 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 174 average time/residue: 0.3707 time to fit residues: 109.3527 Evaluate side-chains 150 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2940 time to fit residues: 17.7546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 282 optimal weight: 30.0000 chunk 157 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 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 705 GLN C 175 ASN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 29381 Z= 0.148 Angle : 0.542 11.569 39827 Z= 0.275 Chirality : 0.041 0.305 4514 Planarity : 0.003 0.054 5010 Dihedral : 4.862 106.958 3876 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3510 helix: 1.68 (0.14), residues: 1523 sheet: 0.50 (0.22), residues: 560 loop : -1.70 (0.16), residues: 1427 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 155 average time/residue: 0.4041 time to fit residues: 106.0877 Evaluate side-chains 134 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3042 time to fit residues: 8.8417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 286 optimal weight: 40.0000 chunk 190 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 443 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN D 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 29381 Z= 0.363 Angle : 0.609 11.806 39827 Z= 0.311 Chirality : 0.043 0.307 4514 Planarity : 0.004 0.050 5010 Dihedral : 4.962 108.209 3876 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.05 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3510 helix: 1.57 (0.14), residues: 1533 sheet: 0.37 (0.22), residues: 548 loop : -1.76 (0.16), residues: 1429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 0.3862 time to fit residues: 94.2910 Evaluate side-chains 134 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 3.293 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3074 time to fit residues: 10.2964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 29381 Z= 0.166 Angle : 0.552 12.597 39827 Z= 0.279 Chirality : 0.041 0.304 4514 Planarity : 0.003 0.059 5010 Dihedral : 4.790 106.125 3876 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3510 helix: 1.69 (0.14), residues: 1527 sheet: 0.45 (0.22), residues: 560 loop : -1.69 (0.16), residues: 1423 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 141 average time/residue: 0.4183 time to fit residues: 97.9940 Evaluate side-chains 131 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 3.199 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2427 time to fit residues: 5.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 285 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN K 755 ASN K1190 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 29381 Z= 0.414 Angle : 0.642 12.006 39827 Z= 0.329 Chirality : 0.044 0.315 4514 Planarity : 0.004 0.050 5010 Dihedral : 4.994 107.808 3876 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3510 helix: 1.53 (0.14), residues: 1531 sheet: 0.32 (0.22), residues: 547 loop : -1.81 (0.16), residues: 1432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 130 average time/residue: 0.4288 time to fit residues: 94.6643 Evaluate side-chains 124 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2896 time to fit residues: 6.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 8.9990 chunk 207 optimal weight: 0.0040 chunk 334 optimal weight: 0.0770 chunk 204 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 350 optimal weight: 0.6980 chunk 322 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.7554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 443 GLN ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29381 Z= 0.202 Angle : 0.585 12.715 39827 Z= 0.297 Chirality : 0.041 0.309 4514 Planarity : 0.004 0.061 5010 Dihedral : 4.868 105.806 3876 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3510 helix: 1.62 (0.14), residues: 1531 sheet: 0.45 (0.22), residues: 554 loop : -1.76 (0.16), residues: 1425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7020 Ramachandran restraints generated. 3510 Oldfield, 0 Emsley, 3510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.4148 time to fit residues: 90.4300 Evaluate side-chains 125 residues out of total 3116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 3.523 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2582 time to fit residues: 5.0272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 0.1980 chunk 221 optimal weight: 4.9990 chunk 297 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 257 optimal weight: 0.0370 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 0.0270 chunk 287 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1272 ASN ** K1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.093287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057543 restraints weight = 100052.642| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.75 r_work: 0.2768 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 29381 Z= 0.137 Angle : 0.559 12.890 39827 Z= 0.280 Chirality : 0.040 0.299 4514 Planarity : 0.003 0.050 5010 Dihedral : 4.590 105.322 3876 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3510 helix: 1.76 (0.14), residues: 1518 sheet: 0.57 (0.22), residues: 564 loop : -1.68 (0.16), residues: 1428 =============================================================================== Job complete usr+sys time: 5119.59 seconds wall clock time: 94 minutes 51.01 seconds (5691.01 seconds total)