Starting phenix.real_space_refine (version: dev) on Wed Mar 15 01:10:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/03_2023/6c24_7335_updated.pdb" } resolution = 3.5 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= 0.011 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 Process input model Symmetric amino acids flipped Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 685": "NH1" <-> "NH2" Residue "K PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13346 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 867 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 52 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 184 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "K" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2406 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 16, 'TRANS': 308} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2881 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 349} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "N" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3062 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "O" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 51 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 484 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 58} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Q" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 496 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 63} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Z" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 674 Classifications: {'peptide': 135} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 134} Link IDs: {'TRANS': 134} Chain breaks: 5 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 407 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 135} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1227 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain breaks: 3 Time building chain proxies: 7.70, per 1000 atoms: 0.58 Number of scatterers: 13346 At special positions: 0 Unit cell: (153.72, 109.2, 109.2, 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 87 16.00 O 2465 8.00 N 2372 7.00 C 8422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 453 " distance=2.09 Simple disulfide: pdb=" SG CYS K 289 " - pdb=" SG CYS K 294 " distance=2.02 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 547 " distance=2.04 Simple disulfide: pdb=" SG CYS K 523 " - pdb=" SG CYS K 549 " distance=2.05 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 549 " distance=2.04 Simple disulfide: pdb=" SG CYS K 530 " - pdb=" SG CYS K 553 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 429 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 1.9 seconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 20 sheets defined 19.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'K' and resid 275 through 277 No H-bonds generated for 'chain 'K' and resid 275 through 277' Processing helix chain 'K' and resid 279 through 283 Processing helix chain 'K' and resid 436 through 447 removed outlier: 3.946A pdb=" N GLY K 445 " --> pdb=" O ARG K 441 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR K 446 " --> pdb=" O VAL K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 457 Processing helix chain 'K' and resid 463 through 475 Processing helix chain 'K' and resid 535 through 538 No H-bonds generated for 'chain 'K' and resid 535 through 538' Processing helix chain 'K' and resid 572 through 574 No H-bonds generated for 'chain 'K' and resid 572 through 574' Processing helix chain 'K' and resid 605 through 608 No H-bonds generated for 'chain 'K' and resid 605 through 608' Processing helix chain 'K' and resid 648 through 661 removed outlier: 3.620A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 683 through 686 Processing helix chain 'L' and resid 268 through 279 Processing helix chain 'M' and resid 576 through 578 No H-bonds generated for 'chain 'M' and resid 576 through 578' Processing helix chain 'M' and resid 592 through 600 Processing helix chain 'M' and resid 608 through 624 Processing helix chain 'M' and resid 630 through 650 removed outlier: 4.520A pdb=" N MET M 637 " --> pdb=" O ASN M 633 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN M 645 " --> pdb=" O GLU M 641 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS M 646 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 653 through 666 removed outlier: 3.720A pdb=" N PHE M 666 " --> pdb=" O SER M 662 " (cutoff:3.500A) Processing helix chain 'M' and resid 671 through 681 Processing helix chain 'N' and resid 6 through 31 removed outlier: 4.061A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N 12 " --> pdb=" O PHE N 8 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE N 23 " --> pdb=" O GLU N 19 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 356 through 361 Processing helix chain 'P' and resid 244 through 256 Proline residue: P 250 - end of helix Processing helix chain 'P' and resid 278 through 280 No H-bonds generated for 'chain 'P' and resid 278 through 280' Processing helix chain 'Q' and resid 83 through 104 removed outlier: 4.197A pdb=" N LYS Q 92 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) Proline residue: Q 93 - end of helix removed outlier: 3.708A pdb=" N ILE Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR Q 97 " --> pdb=" O PRO Q 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 150 No H-bonds generated for 'chain 'Z' and resid 148 through 150' Processing helix chain 'C' and resid 15 through 62 removed outlier: 3.951A pdb=" N GLN C 28 " --> pdb=" O MET C 24 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG C 31 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 179 Processing helix chain 'C' and resid 220 through 223 Processing helix chain 'C' and resid 237 through 246 Processing sheet with id= A, first strand: chain 'A' and resid 474 through 477 Processing sheet with id= B, first strand: chain 'K' and resid 614 through 618 Processing sheet with id= C, first strand: chain 'K' and resid 644 through 646 Processing sheet with id= D, first strand: chain 'K' and resid 695 through 702 removed outlier: 3.603A pdb=" N SER K 639 " --> pdb=" O ILE K 710 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA K 712 " --> pdb=" O PHE K 637 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE K 637 " --> pdb=" O ALA K 712 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 82 through 84 Processing sheet with id= F, first strand: chain 'L' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.796A pdb=" N THR L 153 " --> pdb=" O LEU L 162 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY L 167 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS L 184 " --> pdb=" O ILE L 174 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 193 through 196 removed outlier: 6.926A pdb=" N VAL L 209 " --> pdb=" O ASN L 194 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU L 196 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU L 207 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN L 219 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU L 225 " --> pdb=" O ASN L 219 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 260 through 263 removed outlier: 3.791A pdb=" N ILE L 251 " --> pdb=" O TRP L 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 312 through 315 Processing sheet with id= K, first strand: chain 'L' and resid 331 through 333 Processing sheet with id= L, first strand: chain 'L' and resid 368 through 370 Processing sheet with id= M, first strand: chain 'L' and resid 413 through 418 removed outlier: 7.266A pdb=" N VAL L 428 " --> pdb=" O ARG L 414 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR L 416 " --> pdb=" O ILE L 426 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE L 426 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 61 through 65 removed outlier: 3.852A pdb=" N LEU N 86 " --> pdb=" O SER N 62 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS N 64 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE N 119 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 183 through 185 Processing sheet with id= P, first strand: chain 'N' and resid 202 through 204 Processing sheet with id= Q, first strand: chain 'N' and resid 267 through 270 removed outlier: 4.139A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER N 234 " --> pdb=" O GLY N 244 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'N' and resid 342 through 344 Processing sheet with id= S, first strand: chain 'N' and resid 32 through 39 removed outlier: 6.160A pdb=" N GLN N 403 " --> pdb=" O ASP N 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL N 35 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL N 401 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR N 37 " --> pdb=" O MET N 399 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET N 399 " --> pdb=" O THR N 37 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP N 379 " --> pdb=" O VAL N 393 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'N' and resid 320 through 325 removed outlier: 6.899A pdb=" N SER N 336 " --> pdb=" O PHE N 321 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL N 323 " --> pdb=" O ALA N 334 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA N 334 " --> pdb=" O VAL N 323 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 810 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: 3.54 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 10897 1.53 - 1.86: 2744 1.86 - 2.20: 0 2.20 - 2.54: 0 2.54 - 2.87: 1 Bond restraints: 13642 Sorted by residual: bond pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 1.329 2.875 -1.546 1.40e-02 5.10e+03 1.22e+04 bond pdb=" C GLY Q 146 " pdb=" O GLY Q 146 " ideal model delta sigma weight residual 1.231 1.570 -0.339 2.00e-02 2.50e+03 2.87e+02 bond pdb=" N GLY Q 146 " pdb=" CA GLY Q 146 " ideal model delta sigma weight residual 1.451 1.561 -0.110 1.60e-02 3.91e+03 4.69e+01 bond pdb=" CA GLY Q 146 " pdb=" C GLY Q 146 " ideal model delta sigma weight residual 1.516 1.637 -0.121 1.80e-02 3.09e+03 4.52e+01 bond pdb=" CA ALA N 334 " pdb=" C ALA N 334 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.24e-02 6.50e+03 3.14e+01 ... (remaining 13637 not shown) Histogram of bond angle deviations from ideal: 68.39 - 84.78: 1 84.78 - 101.18: 24 101.18 - 117.58: 10329 117.58 - 133.97: 8172 133.97 - 150.37: 9 Bond angle restraints: 18535 Sorted by residual: angle pdb=" O UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 123.00 68.39 54.61 1.60e+00 3.91e-01 1.17e+03 angle pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " ideal model delta sigma weight residual 116.20 150.37 -34.17 2.00e+00 2.50e-01 2.92e+02 angle pdb=" N THR L 405 " pdb=" CA THR L 405 " pdb=" C THR L 405 " ideal model delta sigma weight residual 108.45 126.25 -17.80 1.26e+00 6.30e-01 2.00e+02 angle pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " pdb=" CA UNK Z 30 " ideal model delta sigma weight residual 121.70 105.49 16.21 1.80e+00 3.09e-01 8.11e+01 angle pdb=" N SER C 73 " pdb=" CA SER C 73 " pdb=" C SER C 73 " ideal model delta sigma weight residual 107.99 92.82 15.17 1.76e+00 3.23e-01 7.43e+01 ... (remaining 18530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.79: 7945 25.79 - 51.57: 212 51.57 - 77.36: 14 77.36 - 103.15: 2 103.15 - 128.93: 1 Dihedral angle restraints: 8174 sinusoidal: 2970 harmonic: 5204 Sorted by residual: dihedral pdb=" CA UNK Z 25 " pdb=" C UNK Z 25 " pdb=" N UNK Z 30 " pdb=" CA UNK Z 30 " ideal model delta harmonic sigma weight residual -180.00 -51.07 -128.93 0 5.00e+00 4.00e-02 6.65e+02 dihedral pdb=" CA MET M 579 " pdb=" C MET M 579 " pdb=" N GLU M 580 " pdb=" CA GLU M 580 " ideal model delta harmonic sigma weight residual 180.00 137.74 42.26 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CB CYS K 530 " pdb=" SG CYS K 530 " pdb=" SG CYS K 549 " pdb=" CB CYS K 549 " ideal model delta sinusoidal sigma weight residual 93.00 166.44 -73.44 1 1.00e+01 1.00e-02 6.86e+01 ... (remaining 8171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1707 0.111 - 0.221: 317 0.221 - 0.332: 44 0.332 - 0.443: 4 0.443 - 0.554: 4 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR L 148 " pdb=" N TYR L 148 " pdb=" C TYR L 148 " pdb=" CB TYR L 148 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CA THR L 405 " pdb=" N THR L 405 " pdb=" C THR L 405 " pdb=" CB THR L 405 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CA ASP E 156 " pdb=" N ASP E 156 " pdb=" C ASP E 156 " pdb=" CB ASP E 156 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 2073 not shown) Planarity restraints: 2403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK Z 25 " -0.150 2.00e-02 2.50e+03 1.64e-01 2.70e+02 pdb=" C UNK Z 25 " 0.278 2.00e-02 2.50e+03 pdb=" O UNK Z 25 " -0.064 2.00e-02 2.50e+03 pdb=" N UNK Z 30 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 151 " 0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO E 152 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 148 " 0.043 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR L 148 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR L 148 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR L 148 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 148 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 148 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR L 148 " 0.020 2.00e-02 2.50e+03 ... (remaining 2400 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 14 1.98 - 2.71: 773 2.71 - 3.44: 19067 3.44 - 4.17: 30462 4.17 - 4.90: 53788 Nonbonded interactions: 104104 Sorted by model distance: nonbonded pdb=" CE1 TYR A 461 " pdb=" O GLU A 542 " model vdw 1.246 3.340 nonbonded pdb=" CE1 HIS K 689 " pdb=" NE2 GLN K 730 " model vdw 1.258 3.340 nonbonded pdb=" CE2 TYR A 461 " pdb=" CB GLU A 542 " model vdw 1.381 3.740 nonbonded pdb=" NE2 HIS N 157 " pdb=" OD2 ASP N 170 " model vdw 1.553 2.520 nonbonded pdb=" CD1 TYR A 461 " pdb=" O GLU A 542 " model vdw 1.598 3.340 ... (remaining 104099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8422 2.51 5 N 2372 2.21 5 O 2465 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.190 Check model and map are aligned: 0.210 Process input model: 35.190 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.017 1.546 13642 Z= 0.886 Angle : 1.564 54.613 18535 Z= 0.960 Chirality : 0.089 0.554 2076 Planarity : 0.007 0.164 2403 Dihedral : 12.276 128.934 4745 Min Nonbonded Distance : 1.246 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 1.50 % Allowed : 15.56 % Favored : 82.94 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.52 % 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: -4.74 (0.18), residues: 1600 helix: -1.89 (0.25), residues: 338 sheet: -3.49 (0.25), residues: 313 loop : -3.67 (0.17), residues: 949 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 412 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 430 average time/residue: 0.3147 time to fit residues: 184.4332 Evaluate side-chains 251 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 238 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1552 time to fit residues: 5.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 GLN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 64 HIS N 88 ASN N 192 HIS N 226 HIS N 239 HIS N 311 HIS ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS P 290 GLN Q 122 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 13642 Z= 0.217 Angle : 0.755 12.082 18535 Z= 0.390 Chirality : 0.048 0.287 2076 Planarity : 0.004 0.054 2403 Dihedral : 6.952 45.912 1878 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.50 % Favored : 91.06 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.19), residues: 1600 helix: -0.59 (0.27), residues: 344 sheet: -3.02 (0.26), residues: 306 loop : -3.03 (0.19), residues: 950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 281 time to evaluate : 1.481 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: 39 outliers final: 22 residues processed: 307 average time/residue: 0.2660 time to fit residues: 119.9071 Evaluate side-chains 245 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1674 time to fit residues: 9.4562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS K 730 GLN ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 HIS N 272 HIS Q 122 ASN C 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 13642 Z= 0.413 Angle : 0.792 11.021 18535 Z= 0.407 Chirality : 0.049 0.237 2076 Planarity : 0.005 0.047 2403 Dihedral : 6.785 44.399 1878 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.81 % Favored : 87.81 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.20), residues: 1600 helix: -0.34 (0.28), residues: 348 sheet: -2.88 (0.26), residues: 310 loop : -2.88 (0.19), residues: 942 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 245 time to evaluate : 1.503 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: 56 outliers final: 31 residues processed: 282 average time/residue: 0.2736 time to fit residues: 110.8139 Evaluate side-chains 253 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1332 time to fit residues: 9.6430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 104 optimal weight: 0.0470 chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 0.4980 chunk 81 optimal weight: 0.1980 chunk 147 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN M 599 GLN M 620 HIS N 176 HIS ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13642 Z= 0.184 Angle : 0.660 9.848 18535 Z= 0.336 Chirality : 0.044 0.236 2076 Planarity : 0.004 0.047 2403 Dihedral : 6.042 40.555 1878 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.06 % Favored : 91.56 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.32 % 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: -2.91 (0.20), residues: 1600 helix: 0.26 (0.29), residues: 338 sheet: -2.66 (0.26), residues: 325 loop : -2.61 (0.19), residues: 937 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 252 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 266 average time/residue: 0.2541 time to fit residues: 97.7875 Evaluate side-chains 234 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 223 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1221 time to fit residues: 4.4653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 41 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN L 349 ASN M 642 ASN ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS Q 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13642 Z= 0.200 Angle : 0.647 9.340 18535 Z= 0.328 Chirality : 0.044 0.173 2076 Planarity : 0.004 0.038 2403 Dihedral : 5.730 39.177 1878 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.00 % Favored : 90.62 % Rotamer Outliers : 2.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.70 (0.20), residues: 1600 helix: 0.39 (0.29), residues: 338 sheet: -2.38 (0.28), residues: 294 loop : -2.53 (0.18), residues: 968 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 246 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 263 average time/residue: 0.2672 time to fit residues: 101.6708 Evaluate side-chains 234 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1284 time to fit residues: 6.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN Q 122 ASN C 69 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 13642 Z= 0.323 Angle : 0.700 10.599 18535 Z= 0.356 Chirality : 0.047 0.319 2076 Planarity : 0.004 0.040 2403 Dihedral : 5.885 40.100 1878 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.69 % Favored : 90.00 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.78 (0.20), residues: 1600 helix: 0.41 (0.29), residues: 337 sheet: -2.64 (0.26), residues: 315 loop : -2.51 (0.19), residues: 948 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 247 average time/residue: 0.2505 time to fit residues: 90.7024 Evaluate side-chains 226 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1347 time to fit residues: 5.7256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 5.9990 chunk 18 optimal weight: 0.0870 chunk 94 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 127 HIS ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN L 349 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 642 ASN Q 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 13642 Z= 0.310 Angle : 0.706 10.878 18535 Z= 0.358 Chirality : 0.046 0.262 2076 Planarity : 0.004 0.038 2403 Dihedral : 5.885 38.561 1878 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.06 % Favored : 89.62 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.76 (0.20), residues: 1600 helix: 0.39 (0.29), residues: 338 sheet: -2.54 (0.26), residues: 309 loop : -2.53 (0.19), residues: 953 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 235 average time/residue: 0.2657 time to fit residues: 91.3681 Evaluate side-chains 222 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1276 time to fit residues: 5.9025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13642 Z= 0.168 Angle : 0.644 11.082 18535 Z= 0.326 Chirality : 0.043 0.197 2076 Planarity : 0.004 0.056 2403 Dihedral : 5.415 36.509 1878 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.19 % Favored : 91.56 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.47 (0.20), residues: 1600 helix: 0.51 (0.29), residues: 345 sheet: -2.25 (0.28), residues: 299 loop : -2.36 (0.19), residues: 956 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 252 average time/residue: 0.2588 time to fit residues: 95.1250 Evaluate side-chains 227 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 221 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1695 time to fit residues: 3.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 20.0000 chunk 157 optimal weight: 0.9990 chunk 144 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 272 ASN ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN L 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 13642 Z= 0.294 Angle : 0.715 12.161 18535 Z= 0.362 Chirality : 0.046 0.310 2076 Planarity : 0.004 0.045 2403 Dihedral : 5.635 36.158 1878 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.94 % Favored : 89.75 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.59 (0.20), residues: 1600 helix: 0.49 (0.29), residues: 343 sheet: -2.44 (0.26), residues: 328 loop : -2.39 (0.19), residues: 929 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 220 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 228 average time/residue: 0.2670 time to fit residues: 88.4120 Evaluate side-chains 222 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 211 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1229 time to fit residues: 4.5336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 170 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN L 360 GLN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN ** N 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 385 ASN Q 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 13642 Z= 0.353 Angle : 0.765 12.708 18535 Z= 0.388 Chirality : 0.047 0.277 2076 Planarity : 0.004 0.041 2403 Dihedral : 5.894 35.233 1878 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.56 % Favored : 89.12 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % 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: -2.69 (0.20), residues: 1600 helix: 0.41 (0.29), residues: 341 sheet: -2.45 (0.26), residues: 332 loop : -2.48 (0.19), residues: 927 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 223 average time/residue: 0.2595 time to fit residues: 84.7459 Evaluate side-chains 215 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1411 time to fit residues: 3.3390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.0670 chunk 56 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 0.3980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 607 GLN ** L 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN ** N 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.151361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.117961 restraints weight = 21912.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118430 restraints weight = 12004.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.119640 restraints weight = 10802.282| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5294 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: