Starting phenix.real_space_refine on Mon Apr 8 11:25:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/04_2024/6c24_7335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/04_2024/6c24_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_7335/04_2024/6c24_7335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/04_2024/6c24_7335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/04_2024/6c24_7335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/04_2024/6c24_7335_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5288/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: 7.20, per 1000 atoms: 0.54 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: 5.24 Conformation dependent library (CDL) restraints added in 2.3 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: 2.57 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: 3.99 Time building geometry restraints manager: 5.74 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 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: 0.970 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: 5.950 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.450 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 % Allowed : 5.32 % Favored : 92.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP N 49 HIS 0.016 0.003 HIS A 466 PHE 0.037 0.005 PHE L 229 TYR 0.043 0.004 TYR L 148 ARG 0.008 0.001 ARG L 169 *********************** 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 : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8847 (mmtp) REVERT: K 452 CYS cc_start: 0.6545 (m) cc_final: 0.6313 (p) REVERT: K 548 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7592 (tm-30) REVERT: K 610 SER cc_start: 0.8293 (m) cc_final: 0.7851 (p) REVERT: K 680 LYS cc_start: 0.9222 (ptpt) cc_final: 0.8808 (ptpp) REVERT: K 721 GLU cc_start: 0.8818 (tt0) cc_final: 0.8548 (tt0) REVERT: K 726 TYR cc_start: 0.8591 (m-10) cc_final: 0.7925 (m-80) REVERT: K 727 ARG cc_start: 0.8115 (ttt180) cc_final: 0.7901 (mtp85) REVERT: L 94 GLN cc_start: 0.8515 (mp10) cc_final: 0.8276 (mm110) REVERT: L 195 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8492 (mm-30) REVERT: L 251 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8542 (mt) REVERT: L 292 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8056 (tp40) REVERT: L 294 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8767 (mt) REVERT: L 307 ASN cc_start: 0.8023 (t0) cc_final: 0.7564 (m-40) REVERT: L 325 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8252 (mm-30) REVERT: L 435 TRP cc_start: 0.8434 (m100) cc_final: 0.8051 (m100) REVERT: M 620 HIS cc_start: 0.8213 (t-90) cc_final: 0.7908 (t-170) REVERT: M 622 MET cc_start: 0.8697 (mtt) cc_final: 0.8463 (mmt) REVERT: M 631 GLN cc_start: 0.7782 (mt0) cc_final: 0.7553 (mt0) REVERT: M 642 ASN cc_start: 0.8476 (m110) cc_final: 0.7967 (m-40) REVERT: M 665 ASP cc_start: 0.8702 (m-30) cc_final: 0.8434 (m-30) REVERT: M 675 ASP cc_start: 0.8837 (t0) cc_final: 0.8609 (p0) REVERT: N 55 ARG cc_start: 0.8247 (pmm-80) cc_final: 0.7575 (ttt180) REVERT: N 85 GLN cc_start: 0.8386 (tt0) cc_final: 0.8134 (mt0) REVERT: N 119 ILE cc_start: 0.8356 (tt) cc_final: 0.8091 (pt) REVERT: N 132 TYR cc_start: 0.9052 (p90) cc_final: 0.8739 (p90) REVERT: N 159 SER cc_start: 0.8280 (m) cc_final: 0.7599 (t) REVERT: N 238 LEU cc_start: 0.9086 (mt) cc_final: 0.8790 (mt) REVERT: N 250 GLN cc_start: 0.8311 (mt0) cc_final: 0.7870 (mp10) REVERT: N 251 LYS cc_start: 0.8430 (mttp) cc_final: 0.8228 (mtpp) REVERT: N 305 ASN cc_start: 0.8488 (t0) cc_final: 0.8242 (t0) REVERT: N 308 LEU cc_start: 0.8998 (tp) cc_final: 0.8780 (tp) REVERT: Q 120 HIS cc_start: 0.8561 (m-70) cc_final: 0.8326 (m170) REVERT: C 50 LEU cc_start: 0.9262 (tt) cc_final: 0.8868 (mm) REVERT: C 104 VAL cc_start: 0.7933 (t) cc_final: 0.7644 (m) outliers start: 23 outliers final: 13 residues processed: 430 average time/residue: 0.3178 time to fit residues: 186.5568 Evaluate side-chains 269 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 386 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 279 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 393 VAL Chi-restraints excluded: chain N residue 401 VAL 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: 0.9980 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: 0.6980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 GLN N 18 ASN N 64 HIS N 88 ASN N 192 HIS N 200 HIS N 226 HIS N 311 HIS ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS P 290 GLN ** Q 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2961 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= 0.211 Angle : 0.740 12.138 18535 Z= 0.381 Chirality : 0.047 0.280 2076 Planarity : 0.004 0.055 2403 Dihedral : 7.463 48.730 1905 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.31 % Favored : 91.25 % Rotamer: Outliers : 3.12 % Allowed : 13.83 % Favored : 83.05 % 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: -0.56 (0.27), residues: 343 sheet: -3.06 (0.26), residues: 308 loop : -3.01 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 24 HIS 0.008 0.001 HIS P 242 PHE 0.023 0.002 PHE K 469 TYR 0.025 0.002 TYR L 148 ARG 0.004 0.001 ARG C 33 *********************** 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 338 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8847 (mmtp) REVERT: K 306 TYR cc_start: 0.3375 (t80) cc_final: 0.1605 (t80) REVERT: K 610 SER cc_start: 0.8264 (m) cc_final: 0.7891 (p) REVERT: K 639 SER cc_start: 0.8032 (t) cc_final: 0.7683 (m) REVERT: K 650 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8415 (mm-30) REVERT: K 721 GLU cc_start: 0.8826 (tt0) cc_final: 0.8461 (tt0) REVERT: L 88 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7589 (tt) REVERT: L 94 GLN cc_start: 0.8649 (mp10) cc_final: 0.8355 (mm110) REVERT: L 119 ASN cc_start: 0.8546 (p0) cc_final: 0.7983 (p0) REVERT: L 155 ASP cc_start: 0.8935 (t0) cc_final: 0.8640 (t0) REVERT: L 169 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7186 (ttm-80) REVERT: L 180 MET cc_start: 0.7911 (mtt) cc_final: 0.7605 (mtm) REVERT: L 238 GLU cc_start: 0.8628 (pt0) cc_final: 0.8416 (pt0) REVERT: L 251 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8653 (mt) REVERT: L 307 ASN cc_start: 0.8063 (t0) cc_final: 0.7778 (m-40) REVERT: L 325 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8222 (mm-30) REVERT: L 385 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7868 (ptpt) REVERT: M 599 GLN cc_start: 0.8916 (tt0) cc_final: 0.8666 (tt0) REVERT: M 623 LYS cc_start: 0.9025 (ttmm) cc_final: 0.8823 (ttmt) REVERT: M 641 GLU cc_start: 0.8936 (tt0) cc_final: 0.8725 (pt0) REVERT: M 643 TYR cc_start: 0.8305 (m-80) cc_final: 0.8097 (m-80) REVERT: M 662 SER cc_start: 0.8974 (t) cc_final: 0.8709 (p) REVERT: N 19 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8519 (mm-30) REVERT: N 85 GLN cc_start: 0.8474 (tt0) cc_final: 0.8181 (mt0) REVERT: N 238 LEU cc_start: 0.9082 (mt) cc_final: 0.8802 (mt) REVERT: N 250 GLN cc_start: 0.7799 (mt0) cc_final: 0.7557 (mp10) REVERT: N 305 ASN cc_start: 0.8401 (t0) cc_final: 0.8170 (t0) REVERT: N 360 GLU cc_start: 0.8384 (tp30) cc_final: 0.8029 (mt-10) REVERT: C 50 LEU cc_start: 0.9123 (tt) cc_final: 0.8785 (mm) REVERT: C 104 VAL cc_start: 0.8046 (t) cc_final: 0.7827 (m) REVERT: C 222 LYS cc_start: 0.6154 (ttpp) cc_final: 0.5616 (ptmt) outliers start: 41 outliers final: 22 residues processed: 323 average time/residue: 0.2569 time to fit residues: 120.4437 Evaluate side-chains 270 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 245 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain M residue 647 ILE Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 168 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN ** L 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 HIS N 239 HIS Q 122 ASN C 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13642 Z= 0.293 Angle : 0.714 10.542 18535 Z= 0.366 Chirality : 0.046 0.217 2076 Planarity : 0.004 0.044 2403 Dihedral : 6.995 53.436 1890 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.38 % Favored : 89.25 % Rotamer: Outliers : 5.02 % Allowed : 15.65 % Favored : 79.33 % 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: -3.23 (0.20), residues: 1600 helix: -0.12 (0.28), residues: 344 sheet: -2.85 (0.26), residues: 297 loop : -2.82 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 432 HIS 0.010 0.001 HIS K 282 PHE 0.021 0.002 PHE K 469 TYR 0.030 0.002 TYR L 148 ARG 0.007 0.001 ARG E 150 *********************** 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 324 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 258 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8906 (mmtp) REVERT: A 474 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7751 (p90) REVERT: K 639 SER cc_start: 0.8029 (t) cc_final: 0.7623 (m) REVERT: K 721 GLU cc_start: 0.8856 (tt0) cc_final: 0.8509 (tt0) REVERT: L 88 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7678 (tt) REVERT: L 94 GLN cc_start: 0.8599 (mp10) cc_final: 0.8320 (mm110) REVERT: L 148 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7430 (p90) REVERT: L 155 ASP cc_start: 0.8917 (t0) cc_final: 0.8574 (t70) REVERT: L 307 ASN cc_start: 0.8006 (t0) cc_final: 0.7549 (m110) REVERT: L 325 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8132 (mm-30) REVERT: L 342 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8367 (mmtm) REVERT: M 569 ASP cc_start: 0.8165 (p0) cc_final: 0.7942 (p0) REVERT: M 599 GLN cc_start: 0.8898 (tt0) cc_final: 0.8500 (tt0) REVERT: N 19 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8671 (mm-30) REVERT: N 85 GLN cc_start: 0.8533 (tt0) cc_final: 0.8298 (mt0) REVERT: N 250 GLN cc_start: 0.7867 (mt0) cc_final: 0.7532 (mp10) REVERT: C 34 ARG cc_start: 0.9176 (ttm-80) cc_final: 0.8798 (ttt-90) REVERT: C 50 LEU cc_start: 0.9086 (tt) cc_final: 0.8756 (mm) REVERT: C 55 ILE cc_start: 0.9597 (mm) cc_final: 0.9186 (tp) REVERT: C 59 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8710 (mp0) REVERT: C 104 VAL cc_start: 0.8055 (t) cc_final: 0.7799 (m) REVERT: C 118 GLN cc_start: 0.8884 (pt0) cc_final: 0.8367 (tt0) REVERT: C 222 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5494 (ptmt) outliers start: 66 outliers final: 43 residues processed: 300 average time/residue: 0.2676 time to fit residues: 114.9801 Evaluate side-chains 280 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 342 LYS Chi-restraints excluded: chain L residue 403 THR Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain P residue 293 LEU Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 102 ASN 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: 4.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13642 Z= 0.318 Angle : 0.709 11.068 18535 Z= 0.362 Chirality : 0.046 0.207 2076 Planarity : 0.004 0.044 2403 Dihedral : 6.962 58.182 1890 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.12 % Favored : 89.50 % Rotamer: Outliers : 5.02 % Allowed : 17.71 % Favored : 77.28 % 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: -3.05 (0.20), residues: 1600 helix: 0.26 (0.28), residues: 337 sheet: -2.76 (0.26), residues: 317 loop : -2.75 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 432 HIS 0.015 0.002 HIS K 282 PHE 0.017 0.002 PHE K 469 TYR 0.026 0.002 TYR L 148 ARG 0.010 0.001 ARG C 81 *********************** 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 314 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 248 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9156 (mtmt) cc_final: 0.8905 (mmtp) REVERT: A 474 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7813 (p90) REVERT: K 721 GLU cc_start: 0.8888 (tt0) cc_final: 0.8540 (tt0) REVERT: L 94 GLN cc_start: 0.8547 (mp10) cc_final: 0.8283 (mm110) REVERT: L 148 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7527 (p90) REVERT: L 238 GLU cc_start: 0.8584 (pt0) cc_final: 0.8084 (pt0) REVERT: L 256 MET cc_start: 0.9041 (mtp) cc_final: 0.8736 (mtm) REVERT: L 276 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8619 (mm-30) REVERT: N 18 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8309 (t0) REVERT: N 85 GLN cc_start: 0.8540 (tt0) cc_final: 0.8304 (mt0) REVERT: N 250 GLN cc_start: 0.7976 (mt0) cc_final: 0.7569 (mp10) REVERT: N 305 ASN cc_start: 0.8548 (t0) cc_final: 0.7818 (p0) REVERT: N 306 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7582 (mt) REVERT: P 246 GLU cc_start: 0.8502 (tp30) cc_final: 0.8037 (tp30) REVERT: P 288 MET cc_start: 0.7937 (mmm) cc_final: 0.7622 (mpp) REVERT: C 50 LEU cc_start: 0.9073 (tt) cc_final: 0.8719 (mm) REVERT: C 104 VAL cc_start: 0.8082 (t) cc_final: 0.7863 (m) REVERT: C 222 LYS cc_start: 0.6161 (ttpp) cc_final: 0.5414 (ptmt) outliers start: 66 outliers final: 50 residues processed: 293 average time/residue: 0.2532 time to fit residues: 107.2083 Evaluate side-chains 274 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 273 THR Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 306 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.0980 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 84 optimal weight: 0.0040 chunk 148 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 M 599 GLN M 620 HIS N 177 GLN ** N 316 HIS ** 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: 0.8016 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13642 Z= 0.190 Angle : 0.647 9.820 18535 Z= 0.329 Chirality : 0.043 0.163 2076 Planarity : 0.004 0.051 2403 Dihedral : 6.244 52.820 1889 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.88 % Favored : 90.75 % Rotamer: Outliers : 4.48 % Allowed : 19.00 % Favored : 76.52 % 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: -2.75 (0.20), residues: 1600 helix: 0.48 (0.29), residues: 336 sheet: -2.64 (0.27), residues: 303 loop : -2.51 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 331 HIS 0.012 0.001 HIS K 282 PHE 0.019 0.001 PHE C 32 TYR 0.020 0.001 TYR L 148 ARG 0.011 0.000 ARG C 81 *********************** 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 318 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 259 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9148 (mtmt) cc_final: 0.8935 (mmtp) REVERT: K 261 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8787 (m) REVERT: K 721 GLU cc_start: 0.8819 (tt0) cc_final: 0.8579 (tt0) REVERT: L 94 GLN cc_start: 0.8538 (mp10) cc_final: 0.8246 (mm110) REVERT: L 276 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8591 (mm-30) REVERT: L 294 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8901 (mt) REVERT: N 8 PHE cc_start: 0.8378 (t80) cc_final: 0.7774 (t80) REVERT: N 85 GLN cc_start: 0.8468 (tt0) cc_final: 0.8265 (mt0) REVERT: N 119 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7935 (pt) REVERT: N 250 GLN cc_start: 0.7557 (mt0) cc_final: 0.7165 (mp10) REVERT: N 253 MET cc_start: 0.8440 (mpp) cc_final: 0.8088 (mpp) REVERT: N 360 GLU cc_start: 0.8668 (tp30) cc_final: 0.8058 (tt0) REVERT: N 366 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8577 (tt) REVERT: C 50 LEU cc_start: 0.8993 (tt) cc_final: 0.8675 (mm) REVERT: C 59 GLU cc_start: 0.9072 (pt0) cc_final: 0.8801 (pp20) REVERT: C 222 LYS cc_start: 0.6126 (ttpp) cc_final: 0.5417 (ptmt) outliers start: 59 outliers final: 43 residues processed: 300 average time/residue: 0.2618 time to fit residues: 113.5108 Evaluate side-chains 265 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 303 ASP Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 268 HIS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 86 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 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 HIS L 292 GLN L 349 ASN M 599 GLN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 659 HIS N 177 GLN Q 122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13642 Z= 0.344 Angle : 0.713 10.998 18535 Z= 0.363 Chirality : 0.046 0.194 2076 Planarity : 0.004 0.050 2403 Dihedral : 6.505 48.523 1889 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.50 % Favored : 89.12 % Rotamer: Outliers : 5.62 % Allowed : 19.68 % Favored : 74.70 % 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: -2.80 (0.20), residues: 1600 helix: 0.38 (0.28), residues: 344 sheet: -2.61 (0.26), residues: 311 loop : -2.57 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 432 HIS 0.012 0.002 HIS K 282 PHE 0.016 0.002 PHE K 724 TYR 0.028 0.002 TYR L 148 ARG 0.011 0.001 ARG C 81 *********************** 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 303 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 229 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8908 (mmtp) REVERT: A 474 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7713 (p90) REVERT: K 261 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8092 (m) REVERT: K 276 GLN cc_start: 0.7494 (tp-100) cc_final: 0.6568 (tp-100) REVERT: K 473 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8169 (mp0) REVERT: K 721 GLU cc_start: 0.8924 (tt0) cc_final: 0.8573 (tt0) REVERT: L 148 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7656 (p90) REVERT: L 276 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8669 (mm-30) REVERT: L 307 ASN cc_start: 0.7979 (t0) cc_final: 0.7492 (t0) REVERT: N 8 PHE cc_start: 0.8528 (t80) cc_final: 0.8311 (t80) REVERT: N 85 GLN cc_start: 0.8524 (tt0) cc_final: 0.8301 (mt0) REVERT: N 250 GLN cc_start: 0.8052 (mt0) cc_final: 0.7573 (mp10) REVERT: P 246 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8143 (mm-30) REVERT: C 50 LEU cc_start: 0.9048 (tt) cc_final: 0.8701 (mm) outliers start: 74 outliers final: 56 residues processed: 285 average time/residue: 0.2497 time to fit residues: 104.1165 Evaluate side-chains 276 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain M residue 673 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4529 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= 0.322 Angle : 0.702 10.949 18535 Z= 0.358 Chirality : 0.046 0.196 2076 Planarity : 0.004 0.058 2403 Dihedral : 6.423 47.742 1889 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.06 % Favored : 89.62 % Rotamer: Outliers : 5.70 % Allowed : 19.30 % Favored : 75.00 % 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: -2.74 (0.20), residues: 1600 helix: 0.46 (0.29), residues: 343 sheet: -2.55 (0.27), residues: 308 loop : -2.54 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 331 HIS 0.011 0.001 HIS K 282 PHE 0.015 0.002 PHE K 724 TYR 0.026 0.002 TYR L 148 ARG 0.014 0.001 ARG C 81 *********************** 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 304 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 229 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8897 (mmtp) REVERT: K 261 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8032 (m) REVERT: K 276 GLN cc_start: 0.7477 (tp-100) cc_final: 0.6544 (tp-100) REVERT: K 721 GLU cc_start: 0.8965 (tt0) cc_final: 0.8710 (tt0) REVERT: L 148 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7759 (p90) REVERT: L 256 MET cc_start: 0.9063 (mtp) cc_final: 0.8827 (mtm) REVERT: L 276 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8634 (mm-30) REVERT: L 307 ASN cc_start: 0.7977 (t0) cc_final: 0.7456 (t0) REVERT: N 85 GLN cc_start: 0.8575 (tt0) cc_final: 0.8313 (mt0) REVERT: N 133 MET cc_start: 0.8078 (tmm) cc_final: 0.7833 (tmm) REVERT: N 250 GLN cc_start: 0.8086 (mt0) cc_final: 0.7582 (mp10) REVERT: N 305 ASN cc_start: 0.8418 (t0) cc_final: 0.7554 (p0) REVERT: P 246 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8213 (mm-30) REVERT: P 251 ASP cc_start: 0.8783 (m-30) cc_final: 0.8529 (m-30) REVERT: C 34 ARG cc_start: 0.9339 (ttm170) cc_final: 0.8949 (mmm-85) REVERT: C 50 LEU cc_start: 0.9029 (tt) cc_final: 0.8675 (mm) REVERT: C 222 LYS cc_start: 0.6196 (ttpt) cc_final: 0.5926 (ptmt) outliers start: 75 outliers final: 60 residues processed: 283 average time/residue: 0.2644 time to fit residues: 109.0475 Evaluate side-chains 284 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 222 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain K residue 732 ASP Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 253 SER Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 332 ILE Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 242 HIS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 112 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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** K 730 GLN L 349 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4820 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= 0.172 Angle : 0.648 9.644 18535 Z= 0.330 Chirality : 0.043 0.174 2076 Planarity : 0.004 0.058 2403 Dihedral : 5.867 44.720 1889 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.56 % Favored : 91.19 % Rotamer: Outliers : 4.18 % Allowed : 22.19 % Favored : 73.63 % 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: -2.55 (0.20), residues: 1600 helix: 0.57 (0.29), residues: 343 sheet: -2.39 (0.27), residues: 304 loop : -2.42 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 432 HIS 0.028 0.001 HIS P 242 PHE 0.018 0.001 PHE N 8 TYR 0.016 0.001 TYR L 148 ARG 0.015 0.001 ARG C 81 *********************** 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 304 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 249 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 261 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8031 (m) REVERT: K 276 GLN cc_start: 0.7467 (tp-100) cc_final: 0.6486 (tp-100) REVERT: K 721 GLU cc_start: 0.8850 (tt0) cc_final: 0.8505 (tt0) REVERT: L 122 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8756 (p) REVERT: L 148 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7443 (p90) REVERT: L 251 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8693 (mt) REVERT: N 20 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8159 (pt0) REVERT: N 85 GLN cc_start: 0.8484 (tt0) cc_final: 0.8259 (mt0) REVERT: N 119 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7840 (pt) REVERT: N 250 GLN cc_start: 0.7678 (mt0) cc_final: 0.7324 (mp10) REVERT: N 305 ASN cc_start: 0.8403 (t0) cc_final: 0.7806 (p0) REVERT: N 360 GLU cc_start: 0.8796 (tp30) cc_final: 0.8185 (tt0) REVERT: P 246 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8079 (tp30) REVERT: P 286 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7779 (tmt170) REVERT: C 34 ARG cc_start: 0.9336 (ttm170) cc_final: 0.8977 (mmm-85) REVERT: C 50 LEU cc_start: 0.8995 (tt) cc_final: 0.8683 (mm) REVERT: C 65 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8063 (mm) REVERT: C 102 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7287 (t0) REVERT: C 222 LYS cc_start: 0.6068 (ttpt) cc_final: 0.5578 (ptmt) outliers start: 55 outliers final: 34 residues processed: 283 average time/residue: 0.2646 time to fit residues: 108.7598 Evaluate side-chains 267 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN 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: 8.9990 chunk 144 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.8180 ------------------------------------------------------------------------------- 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 L 349 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 HIS P 242 HIS Q 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13642 Z= 0.251 Angle : 0.677 9.603 18535 Z= 0.345 Chirality : 0.045 0.180 2076 Planarity : 0.004 0.064 2403 Dihedral : 5.777 43.748 1883 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.31 % Favored : 90.38 % Rotamer: Outliers : 3.95 % Allowed : 22.49 % Favored : 73.56 % 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: -2.51 (0.20), residues: 1600 helix: 0.55 (0.29), residues: 343 sheet: -2.28 (0.27), residues: 316 loop : -2.39 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 331 HIS 0.009 0.001 HIS K 282 PHE 0.013 0.002 PHE M 656 TYR 0.021 0.001 TYR L 148 ARG 0.015 0.001 ARG C 81 *********************** 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 277 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 261 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8021 (m) REVERT: K 276 GLN cc_start: 0.7465 (tp-100) cc_final: 0.6486 (tp-100) REVERT: K 579 GLU cc_start: 0.7987 (tp30) cc_final: 0.7656 (tp30) REVERT: K 720 GLU cc_start: 0.8791 (tt0) cc_final: 0.8551 (tt0) REVERT: K 721 GLU cc_start: 0.8898 (tt0) cc_final: 0.8545 (tt0) REVERT: L 148 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7653 (p90) REVERT: N 85 GLN cc_start: 0.8534 (tt0) cc_final: 0.8288 (mt0) REVERT: N 250 GLN cc_start: 0.7798 (mt0) cc_final: 0.7388 (mp10) REVERT: N 305 ASN cc_start: 0.8520 (t0) cc_final: 0.7963 (p0) REVERT: P 246 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8066 (tp30) REVERT: P 286 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7807 (tmt170) REVERT: C 34 ARG cc_start: 0.9352 (ttm170) cc_final: 0.9138 (mmm-85) REVERT: C 50 LEU cc_start: 0.8989 (tt) cc_final: 0.8666 (mm) REVERT: C 222 LYS cc_start: 0.6104 (ttpt) cc_final: 0.5691 (ptmt) outliers start: 52 outliers final: 47 residues processed: 259 average time/residue: 0.2567 time to fit residues: 97.2770 Evaluate side-chains 265 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain K residue 703 ASN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 242 HIS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 283 ASN Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 0.0040 chunk 107 optimal weight: 7.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 L 307 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13642 Z= 0.184 Angle : 0.659 11.623 18535 Z= 0.336 Chirality : 0.044 0.177 2076 Planarity : 0.004 0.065 2403 Dihedral : 5.583 41.157 1883 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.75 % Favored : 91.00 % Rotamer: Outliers : 3.42 % Allowed : 23.02 % Favored : 73.56 % 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: -2.41 (0.20), residues: 1600 helix: 0.56 (0.29), residues: 344 sheet: -2.13 (0.27), residues: 318 loop : -2.35 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 331 HIS 0.008 0.001 HIS K 282 PHE 0.015 0.001 PHE M 656 TYR 0.025 0.001 TYR A 461 ARG 0.015 0.001 ARG C 81 ********************** 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 276 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 231 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 721 GLU cc_start: 0.8823 (tt0) cc_final: 0.8488 (tt0) REVERT: L 148 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7480 (p90) REVERT: N 20 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8186 (pt0) REVERT: N 85 GLN cc_start: 0.8521 (tt0) cc_final: 0.8252 (mt0) REVERT: N 250 GLN cc_start: 0.7534 (mt0) cc_final: 0.7206 (mp10) REVERT: N 305 ASN cc_start: 0.8513 (t0) cc_final: 0.7975 (p0) REVERT: N 360 GLU cc_start: 0.8822 (tp30) cc_final: 0.8216 (tt0) REVERT: P 246 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8021 (tp30) REVERT: P 286 ARG cc_start: 0.7853 (tpt90) cc_final: 0.7640 (tmt170) REVERT: C 34 ARG cc_start: 0.9354 (ttm170) cc_final: 0.9147 (mmm-85) REVERT: C 50 LEU cc_start: 0.8958 (tt) cc_final: 0.8634 (mm) REVERT: C 65 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8078 (mm) REVERT: C 102 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7257 (t0) REVERT: C 222 LYS cc_start: 0.6004 (ttpt) cc_final: 0.5601 (ptmt) outliers start: 45 outliers final: 38 residues processed: 259 average time/residue: 0.2586 time to fit residues: 97.6876 Evaluate side-chains 266 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 225 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 568 THR Chi-restraints excluded: chain K residue 694 ASN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 232 VAL Chi-restraints excluded: chain L residue 237 ASP Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 622 MET Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 168 ASN Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 230 VAL Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 302 ASP Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain P residue 242 HIS Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 102 ASN 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: 5.9990 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** K 648 GLN L 307 ASN ** M 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.148697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.113167 restraints weight = 22022.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114794 restraints weight = 12303.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.115912 restraints weight = 10523.051| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13642 Z= 0.262 Angle : 0.700 17.289 18535 Z= 0.354 Chirality : 0.045 0.204 2076 Planarity : 0.004 0.066 2403 Dihedral : 5.720 43.353 1883 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.56 % Favored : 90.12 % Rotamer: Outliers : 3.88 % Allowed : 23.25 % Favored : 72.87 % 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: -2.40 (0.20), residues: 1600 helix: 0.57 (0.29), residues: 343 sheet: -2.13 (0.27), residues: 318 loop : -2.32 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 331 HIS 0.015 0.001 HIS P 242 PHE 0.020 0.002 PHE M 656 TYR 0.026 0.002 TYR A 461 ARG 0.015 0.001 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.09 seconds wall clock time: 55 minutes 34.78 seconds (3334.78 seconds total)