Starting phenix.real_space_refine on Thu Sep 26 14:38:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/09_2024/6c24_7335.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/09_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_7335/09_2024/6c24_7335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/09_2024/6c24_7335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/09_2024/6c24_7335.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c24_7335/09_2024/6c24_7335.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.18, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 3.31 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 33 helices and 25 sheets defined 23.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.503A pdb=" N LEU A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'K' and resid 274 through 277 Processing helix chain 'K' and resid 278 through 284 Processing helix chain 'K' and resid 435 through 448 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 452 through 458 Processing helix chain 'K' and resid 462 through 476 Processing helix chain 'K' and resid 534 through 539 Processing helix chain 'K' and resid 571 through 575 removed outlier: 3.506A pdb=" N LEU K 575 " --> pdb=" O PRO K 572 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 609 removed outlier: 3.664A pdb=" N ARG K 608 " --> pdb=" O CYS K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 647 through 662 removed outlier: 3.620A pdb=" N VAL K 657 " --> pdb=" O ARG K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 682 through 687 removed outlier: 3.576A pdb=" N ALA K 687 " --> pdb=" O ILE K 684 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 279 Processing helix chain 'M' and resid 575 through 579 Processing helix chain 'M' and resid 591 through 601 Processing helix chain 'M' and resid 607 through 625 Processing helix chain 'M' and resid 629 through 651 removed outlier: 3.663A pdb=" N ASN M 633 " --> pdb=" O ASP M 629 " (cutoff:3.500A) 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 652 through 665 Processing helix chain 'M' and resid 670 through 682 removed outlier: 3.561A pdb=" N ILE M 674 " --> pdb=" O SER M 670 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 27 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) Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 355 through 362 Processing helix chain 'P' and resid 244 through 257 Proline residue: P 250 - end of helix Processing helix chain 'P' and resid 277 through 281 removed outlier: 3.758A pdb=" N ASP P 281 " --> pdb=" O LEU P 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 105 removed outlier: 4.163A pdb=" N PHE Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) 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 147 through 151 removed outlier: 3.693A pdb=" N UNK Z 151 " --> pdb=" O UNK Z 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 63 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) removed outlier: 3.530A pdb=" N ARG C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 180 removed outlier: 3.676A pdb=" N PHE C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.572A pdb=" N LYS C 222 " --> pdb=" O PRO C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.957A pdb=" N SER C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.621A pdb=" N LEU C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 433 removed outlier: 4.349A pdb=" N ILE A 491 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 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=AA3, first strand: chain 'K' and resid 614 through 618 Processing sheet with id=AA4, first strand: chain 'K' and resid 637 through 640 removed outlier: 6.629A pdb=" N PHE K 637 " --> pdb=" O ALA K 712 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA K 712 " --> pdb=" O PHE K 637 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER K 639 " --> pdb=" O ILE K 710 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 645 through 646 Processing sheet with id=AA6, first strand: chain 'K' and resid 680 through 681 Processing sheet with id=AA7, first strand: chain 'K' and resid 688 through 689 removed outlier: 6.519A pdb=" N ASN K 688 " --> pdb=" O PHE K 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 99 through 101 Processing sheet with id=AA9, first strand: chain 'L' and resid 125 through 127 removed outlier: 4.503A pdb=" N GLU L 131 " --> pdb=" O HIS L 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 147 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=AB2, first strand: chain 'L' and resid 195 through 197 removed outlier: 3.580A pdb=" N GLU L 195 " --> pdb=" O VAL L 209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 209 " --> pdb=" O GLU L 195 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS L 197 " --> pdb=" O LEU L 207 " (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=AB3, first strand: chain 'L' and resid 239 through 244 removed outlier: 3.708A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE L 251 " --> pdb=" O TRP L 263 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU L 260 " --> pdb=" O THR L 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 309 through 315 removed outlier: 4.820A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 322 " --> pdb=" O CYS L 311 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY L 354 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 368 through 370 Processing sheet with id=AB6, first strand: chain 'L' and resid 413 through 417 removed outlier: 4.082A pdb=" N GLN L 415 " --> pdb=" O VAL L 428 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER L 417 " --> pdb=" O ILE L 426 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE L 426 " --> pdb=" O SER L 417 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 425 " --> pdb=" O TRP L 437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 565 through 566 removed outlier: 4.787A pdb=" N TYR M 565 " --> pdb=" O LEU M 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 50 through 54 removed outlier: 6.442A pdb=" N ASP N 52 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG N 65 " --> pdb=" O ASP N 52 " (cutoff:3.500A) 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: 4.177A pdb=" N ASN N 77 " --> pdb=" O HIS N 123 " (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=AB9, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AC1, first strand: chain 'N' and resid 183 through 185 removed outlier: 3.714A pdb=" N CYS N 203 " --> pdb=" O SER N 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 230 through 235 removed outlier: 3.907A pdb=" N SER N 234 " --> pdb=" O GLY N 244 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA N 247 " --> pdb=" O LYS N 251 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS N 251 " --> pdb=" O ALA N 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 288 through 289 Processing sheet with id=AC4, first strand: chain 'N' and resid 298 through 299 removed outlier: 3.500A pdb=" N VAL N 298 " --> pdb=" O PHE N 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 320 through 325 removed outlier: 4.200A pdb=" N GLN N 322 " --> pdb=" O SER N 336 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'Z' and resid 59 through 60 removed outlier: 7.159A pdb=" N UNK Z 59 " --> pdb=" O UNK Z 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 352 hydrogen bonds defined for protein. 975 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: 3.80 Time building geometry restraints manager: 3.85 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: 0.00 - 10.92: 18520 10.92 - 21.85: 13 21.85 - 32.77: 0 32.77 - 43.69: 1 43.69 - 54.61: 1 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: 13 1.98 - 2.71: 761 2.71 - 3.44: 18999 3.44 - 4.17: 30327 4.17 - 4.90: 53744 Nonbonded interactions: 103844 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 3.120 nonbonded pdb=" CD1 TYR A 461 " pdb=" O GLU A 542 " model vdw 1.598 3.340 ... (remaining 103839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.940 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.110 ------------------------------------------------------------------------------- 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= 1.175 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 : 1.611 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: 0.3038 time to fit residues: 177.8214 Evaluate side-chains 269 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 157 HIS N 176 HIS N 192 HIS N 200 HIS N 226 HIS N 311 HIS 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13642 Z= 0.229 Angle : 0.781 12.007 18535 Z= 0.404 Chirality : 0.048 0.283 2076 Planarity : 0.004 0.055 2403 Dihedral : 7.617 49.657 1905 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.31 % Favored : 91.19 % Rotamer: Outliers : 3.04 % Allowed : 13.68 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.45 % 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: -3.66 (0.19), residues: 1600 helix: -0.67 (0.27), residues: 348 sheet: -3.00 (0.26), residues: 291 loop : -3.07 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 24 HIS 0.015 0.001 HIS K 689 PHE 0.025 0.002 PHE K 469 TYR 0.023 0.002 TYR K 520 ARG 0.006 0.001 ARG C 34 *********************** 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 337 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 297 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9147 (mtmt) cc_final: 0.8850 (mmtp) REVERT: A 474 PHE cc_start: 0.8060 (p90) cc_final: 0.7786 (p90) REVERT: E 142 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8255 (t) REVERT: K 293 ASP cc_start: 0.7860 (t0) cc_final: 0.7423 (t0) REVERT: K 306 TYR cc_start: 0.3412 (t80) cc_final: 0.1563 (t80) REVERT: K 452 CYS cc_start: 0.6541 (m) cc_final: 0.6331 (p) REVERT: K 548 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7708 (tm-30) REVERT: K 610 SER cc_start: 0.8218 (m) cc_final: 0.7880 (p) REVERT: K 639 SER cc_start: 0.8062 (t) cc_final: 0.7659 (m) REVERT: K 720 GLU cc_start: 0.8871 (tt0) cc_final: 0.8643 (tt0) REVERT: K 721 GLU cc_start: 0.8889 (tt0) cc_final: 0.8597 (tt0) REVERT: L 88 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7482 (tt) REVERT: L 94 GLN cc_start: 0.8573 (mp10) cc_final: 0.8304 (mm110) REVERT: L 155 ASP cc_start: 0.8990 (t0) cc_final: 0.8749 (t70) REVERT: L 169 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7125 (ttm-80) REVERT: L 251 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (mt) REVERT: L 307 ASN cc_start: 0.8060 (t0) cc_final: 0.7701 (m-40) REVERT: L 325 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8193 (mm-30) REVERT: L 385 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7869 (ptpt) REVERT: M 569 ASP cc_start: 0.8144 (p0) cc_final: 0.7835 (p0) REVERT: M 599 GLN cc_start: 0.8884 (tt0) cc_final: 0.8411 (tt0) REVERT: M 623 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8829 (ttmt) REVERT: M 643 TYR cc_start: 0.8298 (m-80) cc_final: 0.8013 (m-80) REVERT: M 662 SER cc_start: 0.9057 (t) cc_final: 0.8795 (p) REVERT: N 19 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8524 (mm-30) REVERT: N 55 ARG cc_start: 0.8380 (pmm-80) cc_final: 0.7661 (ttt180) REVERT: N 85 GLN cc_start: 0.8468 (tt0) cc_final: 0.8137 (mt0) REVERT: N 119 ILE cc_start: 0.8162 (tt) cc_final: 0.7795 (mt) REVERT: N 250 GLN cc_start: 0.7913 (mt0) cc_final: 0.7588 (mp10) REVERT: N 305 ASN cc_start: 0.8478 (t0) cc_final: 0.8143 (t0) REVERT: N 360 GLU cc_start: 0.8400 (tp30) cc_final: 0.7929 (mt-10) REVERT: C 50 LEU cc_start: 0.9132 (tt) cc_final: 0.8795 (mm) REVERT: C 222 LYS cc_start: 0.6167 (ttpp) cc_final: 0.5520 (ptmt) outliers start: 40 outliers final: 19 residues processed: 319 average time/residue: 0.2439 time to fit residues: 113.5207 Evaluate side-chains 279 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain K residue 530 CYS Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 169 ARG Chi-restraints excluded: chain L residue 171 ILE Chi-restraints excluded: chain L residue 187 VAL Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 403 THR 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 222 ILE 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: 7.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 326 ASN N 239 HIS ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN C 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13642 Z= 0.373 Angle : 0.772 11.988 18535 Z= 0.399 Chirality : 0.048 0.222 2076 Planarity : 0.005 0.045 2403 Dihedral : 7.307 53.590 1890 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.81 % Favored : 88.75 % Rotamer: Outliers : 5.02 % Allowed : 15.50 % Favored : 79.48 % 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: -3.32 (0.20), residues: 1600 helix: -0.33 (0.27), residues: 354 sheet: -2.87 (0.26), residues: 309 loop : -2.83 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 432 HIS 0.018 0.002 HIS K 282 PHE 0.022 0.002 PHE K 469 TYR 0.031 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 330 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 264 time to evaluate : 1.620 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: 0.9165 (mtmt) cc_final: 0.8934 (mmtp) REVERT: A 474 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7894 (p90) REVERT: E 142 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8247 (t) REVERT: K 452 CYS cc_start: 0.6898 (m) cc_final: 0.6565 (p) REVERT: K 639 SER cc_start: 0.7999 (t) cc_final: 0.7515 (m) REVERT: K 721 GLU cc_start: 0.8949 (tt0) cc_final: 0.8665 (tt0) REVERT: L 88 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7582 (tt) REVERT: L 94 GLN cc_start: 0.8602 (mp10) cc_final: 0.8359 (mm110) REVERT: L 148 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7586 (p90) REVERT: L 155 ASP cc_start: 0.9008 (t0) cc_final: 0.8662 (t70) REVERT: L 180 MET cc_start: 0.7943 (mtt) cc_final: 0.7489 (mtm) REVERT: L 307 ASN cc_start: 0.8002 (t0) cc_final: 0.7522 (m110) REVERT: L 325 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8005 (mm-30) REVERT: M 622 MET cc_start: 0.8357 (mmm) cc_final: 0.7837 (mtm) REVERT: N 20 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8206 (pt0) REVERT: N 55 ARG cc_start: 0.8365 (pmm-80) cc_final: 0.7803 (ttt180) REVERT: N 250 GLN cc_start: 0.8023 (mt0) cc_final: 0.7584 (mp10) REVERT: N 305 ASN cc_start: 0.8490 (t0) cc_final: 0.8278 (t0) REVERT: N 318 ASP cc_start: 0.8801 (t0) cc_final: 0.8558 (t0) REVERT: P 288 MET cc_start: 0.7993 (mmm) cc_final: 0.7774 (mmt) REVERT: Q 100 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9153 (mp) REVERT: C 34 ARG cc_start: 0.9223 (ttm-80) cc_final: 0.8841 (ttt-90) REVERT: C 50 LEU cc_start: 0.9101 (tt) cc_final: 0.8783 (mm) REVERT: C 222 LYS cc_start: 0.6085 (ttpp) cc_final: 0.5447 (ptmt) outliers start: 66 outliers final: 40 residues processed: 311 average time/residue: 0.2591 time to fit residues: 116.1141 Evaluate side-chains 285 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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 E residue 142 THR 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 661 TYR 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 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 L residue 403 THR 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 119 ILE Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 149 VAL 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 288 ILE 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 252 VAL Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 115 LEU 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: 0.7980 chunk 80 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 30.0000 chunk 44 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 599 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 HIS Q 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13642 Z= 0.277 Angle : 0.704 11.169 18535 Z= 0.363 Chirality : 0.046 0.173 2076 Planarity : 0.004 0.043 2403 Dihedral : 6.857 58.772 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.50 % Favored : 90.12 % Rotamer: Outliers : 4.48 % Allowed : 17.55 % Favored : 77.96 % 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: -3.03 (0.20), residues: 1600 helix: -0.01 (0.28), residues: 347 sheet: -2.68 (0.27), residues: 304 loop : -2.68 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 432 HIS 0.017 0.001 HIS K 282 PHE 0.016 0.002 PHE A 474 TYR 0.022 0.002 TYR L 148 ARG 0.008 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 319 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 260 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8936 (mmtp) REVERT: E 142 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8036 (t) REVERT: K 452 CYS cc_start: 0.7066 (m) cc_final: 0.6751 (p) REVERT: K 639 SER cc_start: 0.8040 (t) cc_final: 0.7618 (m) REVERT: K 721 GLU cc_start: 0.8923 (tt0) cc_final: 0.8581 (tt0) REVERT: L 88 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7493 (tt) REVERT: L 294 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8866 (mt) REVERT: M 603 PHE cc_start: 0.7484 (m-80) cc_final: 0.7195 (m-80) REVERT: N 20 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8182 (pt0) REVERT: N 55 ARG cc_start: 0.8307 (pmm-80) cc_final: 0.7766 (ttt90) REVERT: N 250 GLN cc_start: 0.7831 (mt0) cc_final: 0.7445 (mp10) REVERT: N 305 ASN cc_start: 0.8444 (t0) cc_final: 0.8171 (t0) REVERT: P 246 GLU cc_start: 0.8450 (tp30) cc_final: 0.7956 (tp30) REVERT: C 50 LEU cc_start: 0.9096 (tt) cc_final: 0.8782 (mm) REVERT: C 62 GLN cc_start: 0.9304 (tp40) cc_final: 0.9035 (tm-30) outliers start: 59 outliers final: 34 residues processed: 297 average time/residue: 0.2635 time to fit residues: 112.5088 Evaluate side-chains 266 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 229 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 E residue 142 THR Chi-restraints excluded: chain E residue 145 SER 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 661 TYR Chi-restraints excluded: chain L residue 88 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 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 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 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 269 VAL Chi-restraints excluded: chain N residue 273 THR 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 401 VAL Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 chunk 41 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13642 Z= 0.411 Angle : 0.769 12.402 18535 Z= 0.395 Chirality : 0.048 0.196 2076 Planarity : 0.005 0.051 2403 Dihedral : 6.965 54.494 1889 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.81 % Favored : 87.81 % Rotamer: Outliers : 5.78 % Allowed : 17.48 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.19 % 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: -3.08 (0.20), residues: 1600 helix: 0.00 (0.28), residues: 342 sheet: -2.70 (0.26), residues: 313 loop : -2.72 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 432 HIS 0.016 0.002 HIS K 282 PHE 0.016 0.002 PHE A 474 TYR 0.028 0.002 TYR L 148 ARG 0.012 0.001 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 314 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 238 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8877 (mmtp) REVERT: A 474 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7697 (p90) REVERT: E 142 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8102 (t) REVERT: K 452 CYS cc_start: 0.7111 (m) cc_final: 0.6702 (p) REVERT: K 473 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8063 (mp0) REVERT: K 721 GLU cc_start: 0.8992 (tt0) cc_final: 0.8650 (tt0) REVERT: L 88 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7598 (tt) REVERT: L 111 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7854 (mt) REVERT: L 148 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7904 (p90) REVERT: L 276 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8604 (mm-30) REVERT: L 294 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8851 (mt) REVERT: N 19 GLU cc_start: 0.9202 (tp30) cc_final: 0.8911 (tp30) REVERT: N 20 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8242 (pt0) REVERT: N 55 ARG cc_start: 0.8355 (pmm-80) cc_final: 0.7874 (ttt90) REVERT: N 250 GLN cc_start: 0.8088 (mt0) cc_final: 0.7557 (mp10) REVERT: P 246 GLU cc_start: 0.8451 (tp30) cc_final: 0.7967 (tp30) REVERT: C 50 LEU cc_start: 0.9070 (tt) cc_final: 0.8724 (mm) REVERT: C 62 GLN cc_start: 0.9298 (tp40) cc_final: 0.9039 (tm-30) outliers start: 76 outliers final: 51 residues processed: 294 average time/residue: 0.2625 time to fit residues: 111.4569 Evaluate side-chains 278 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 221 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 E residue 142 THR Chi-restraints excluded: chain E residue 145 SER 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 586 LEU Chi-restraints excluded: chain K residue 661 TYR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 88 LEU 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 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 294 ILE Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain M residue 663 MET Chi-restraints excluded: chain M residue 669 ILE Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 50 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 230 VAL Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 269 VAL Chi-restraints excluded: chain N residue 288 ILE 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 274 LYS Chi-restraints excluded: chain P residue 276 THR Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 548 GLN K 730 GLN L 307 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13642 Z= 0.257 Angle : 0.693 12.167 18535 Z= 0.355 Chirality : 0.045 0.164 2076 Planarity : 0.004 0.051 2403 Dihedral : 6.463 54.198 1889 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.06 % Favored : 90.69 % Rotamer: Outliers : 4.71 % Allowed : 19.68 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.20), residues: 1600 helix: 0.25 (0.29), residues: 342 sheet: -2.60 (0.27), residues: 298 loop : -2.53 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 364 HIS 0.012 0.001 HIS K 282 PHE 0.012 0.001 PHE K 724 TYR 0.021 0.002 TYR L 148 ARG 0.010 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 308 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 246 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9121 (mtmt) cc_final: 0.8882 (mmtp) REVERT: K 261 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8668 (m) REVERT: K 452 CYS cc_start: 0.7086 (m) cc_final: 0.6656 (p) REVERT: K 639 SER cc_start: 0.8005 (t) cc_final: 0.7583 (m) REVERT: K 721 GLU cc_start: 0.8941 (tt0) cc_final: 0.8689 (tt0) REVERT: L 148 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7782 (p90) REVERT: L 276 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8527 (mm-30) REVERT: L 294 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8745 (mp) REVERT: N 8 PHE cc_start: 0.8411 (t80) cc_final: 0.7824 (t80) REVERT: N 19 GLU cc_start: 0.9184 (tp30) cc_final: 0.8873 (tp30) REVERT: N 20 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8224 (pt0) REVERT: N 55 ARG cc_start: 0.8299 (pmm-80) cc_final: 0.7839 (ttt90) REVERT: C 50 LEU cc_start: 0.9058 (tt) cc_final: 0.8731 (mm) REVERT: C 62 GLN cc_start: 0.9280 (tp40) cc_final: 0.9011 (tm-30) REVERT: C 222 LYS cc_start: 0.6037 (ttpt) cc_final: 0.5754 (ptmt) outliers start: 62 outliers final: 45 residues processed: 287 average time/residue: 0.2457 time to fit residues: 102.4326 Evaluate side-chains 274 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 E residue 142 THR Chi-restraints excluded: chain E residue 145 SER 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 661 TYR Chi-restraints excluded: chain L residue 99 VAL 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 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 294 ILE Chi-restraints excluded: chain M residue 579 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 217 VAL Chi-restraints excluded: chain N residue 230 VAL 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 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 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.9990 chunk 18 optimal weight: 30.0000 chunk 94 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 127 HIS L 307 ASN N 135 GLN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13642 Z= 0.292 Angle : 0.719 12.779 18535 Z= 0.365 Chirality : 0.046 0.173 2076 Planarity : 0.004 0.060 2403 Dihedral : 6.373 52.237 1888 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.75 % Favored : 88.94 % Rotamer: Outliers : 5.02 % Allowed : 19.76 % Favored : 75.23 % 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: -2.73 (0.20), residues: 1600 helix: 0.34 (0.29), residues: 342 sheet: -2.51 (0.27), residues: 297 loop : -2.51 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 49 HIS 0.012 0.001 HIS K 282 PHE 0.013 0.001 PHE K 724 TYR 0.025 0.002 TYR K 728 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 301 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 235 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8883 (mmtp) REVERT: K 261 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8760 (m) REVERT: K 452 CYS cc_start: 0.6966 (m) cc_final: 0.6461 (p) REVERT: K 639 SER cc_start: 0.7998 (t) cc_final: 0.7569 (m) REVERT: K 721 GLU cc_start: 0.8969 (tt0) cc_final: 0.8573 (tt0) REVERT: L 148 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7834 (p90) REVERT: L 276 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8512 (mm-30) REVERT: L 294 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8731 (mp) REVERT: N 19 GLU cc_start: 0.9183 (tp30) cc_final: 0.8863 (tp30) REVERT: N 20 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8234 (pt0) REVERT: N 55 ARG cc_start: 0.8328 (pmm-80) cc_final: 0.7867 (ttt90) REVERT: P 246 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8136 (mm-30) REVERT: P 251 ASP cc_start: 0.8802 (m-30) cc_final: 0.8593 (m-30) REVERT: C 50 LEU cc_start: 0.9040 (tt) cc_final: 0.8716 (mm) REVERT: C 62 GLN cc_start: 0.9297 (tp40) cc_final: 0.9042 (tm-30) REVERT: C 222 LYS cc_start: 0.6011 (ttpt) cc_final: 0.5728 (ptmt) outliers start: 66 outliers final: 53 residues processed: 282 average time/residue: 0.2727 time to fit residues: 112.1531 Evaluate side-chains 285 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 E residue 142 THR Chi-restraints excluded: chain E residue 145 SER 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 661 TYR 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 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 290 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 579 MET Chi-restraints excluded: chain M residue 607 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 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 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 269 VAL Chi-restraints excluded: chain N residue 273 THR 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 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 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 15 optimal weight: 20.0000 chunk 129 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** K 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN N 123 HIS N 188 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13642 Z= 0.185 Angle : 0.674 11.977 18535 Z= 0.342 Chirality : 0.044 0.181 2076 Planarity : 0.004 0.062 2403 Dihedral : 5.870 50.845 1888 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.31 % Favored : 91.50 % Rotamer: Outliers : 3.50 % Allowed : 21.58 % Favored : 74.92 % 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: -2.53 (0.20), residues: 1600 helix: 0.45 (0.29), residues: 349 sheet: -2.22 (0.28), residues: 306 loop : -2.43 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 235 HIS 0.009 0.001 HIS K 282 PHE 0.022 0.001 PHE N 8 TYR 0.027 0.001 TYR K 728 ARG 0.017 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 289 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 261 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8796 (m) REVERT: K 452 CYS cc_start: 0.6948 (m) cc_final: 0.6505 (p) REVERT: K 530 CYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6476 (m) REVERT: K 720 GLU cc_start: 0.8913 (tt0) cc_final: 0.8593 (tt0) REVERT: K 721 GLU cc_start: 0.8911 (tt0) cc_final: 0.8541 (tt0) REVERT: L 148 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7765 (p90) REVERT: L 251 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8694 (mt) REVERT: L 276 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8533 (mm-30) REVERT: M 650 LYS cc_start: 0.8782 (tppt) cc_final: 0.8355 (tppt) REVERT: N 20 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8227 (pt0) REVERT: N 55 ARG cc_start: 0.8326 (pmm-80) cc_final: 0.7979 (ttt180) REVERT: P 246 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8077 (tp30) REVERT: C 37 GLU cc_start: 0.8429 (pp20) cc_final: 0.8112 (pp20) REVERT: C 50 LEU cc_start: 0.8968 (tt) cc_final: 0.8638 (mm) REVERT: C 62 GLN cc_start: 0.9252 (tp40) cc_final: 0.8989 (tm-30) REVERT: C 102 ASN cc_start: 0.7746 (m110) cc_final: 0.7288 (t0) REVERT: C 222 LYS cc_start: 0.5940 (ttpt) cc_final: 0.5564 (ptmt) outliers start: 46 outliers final: 29 residues processed: 276 average time/residue: 0.2479 time to fit residues: 99.3422 Evaluate side-chains 262 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 229 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 661 TYR 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 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 251 ILE Chi-restraints excluded: chain M residue 596 THR 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 146 SER 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 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS 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: 7.9990 chunk 144 optimal weight: 30.0000 chunk 153 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 0.1980 chunk 145 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 694 ASN L 307 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 ASN Q 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13642 Z= 0.360 Angle : 0.749 12.805 18535 Z= 0.381 Chirality : 0.046 0.191 2076 Planarity : 0.005 0.086 2403 Dihedral : 6.177 48.335 1886 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.62 % Favored : 89.19 % Rotamer: Outliers : 4.18 % Allowed : 21.66 % Favored : 74.16 % 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 (0.21), residues: 1600 helix: 0.50 (0.29), residues: 349 sheet: -2.21 (0.28), residues: 314 loop : -2.48 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 235 HIS 0.011 0.001 HIS K 282 PHE 0.013 0.002 PHE Q 86 TYR 0.023 0.002 TYR K 728 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 288 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 261 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8795 (m) REVERT: K 452 CYS cc_start: 0.6899 (m) cc_final: 0.6362 (p) REVERT: K 473 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8065 (mp0) REVERT: K 530 CYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6537 (m) REVERT: K 639 SER cc_start: 0.8001 (t) cc_final: 0.7565 (m) REVERT: K 720 GLU cc_start: 0.8885 (tt0) cc_final: 0.8562 (tt0) REVERT: K 721 GLU cc_start: 0.8966 (tt0) cc_final: 0.8576 (tt0) REVERT: L 122 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8868 (p) REVERT: L 148 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7925 (p90) REVERT: L 294 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8700 (mp) REVERT: M 650 LYS cc_start: 0.8763 (tppt) cc_final: 0.8312 (tppt) REVERT: N 20 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8242 (pt0) REVERT: N 55 ARG cc_start: 0.8333 (pmm-80) cc_final: 0.7940 (ttt90) REVERT: P 246 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7988 (tp30) REVERT: C 50 LEU cc_start: 0.9000 (tt) cc_final: 0.8669 (mm) REVERT: C 62 GLN cc_start: 0.9274 (tp40) cc_final: 0.9024 (tm-30) REVERT: C 222 LYS cc_start: 0.5903 (ttpt) cc_final: 0.5512 (ptmt) outliers start: 55 outliers final: 44 residues processed: 270 average time/residue: 0.2284 time to fit residues: 91.1154 Evaluate side-chains 280 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 E residue 145 SER 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 586 LEU Chi-restraints excluded: chain K residue 661 TYR Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain K residue 684 ILE 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 232 VAL Chi-restraints excluded: chain L residue 241 SER Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 290 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 349 ASN Chi-restraints excluded: chain L residue 416 THR Chi-restraints excluded: chain M residue 596 THR 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 86 LEU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 146 SER 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 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 5.9990 chunk 99 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 0.0570 chunk 170 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 607 GLN L 307 ASN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 633 ASN ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13642 Z= 0.191 Angle : 0.692 10.696 18535 Z= 0.351 Chirality : 0.044 0.184 2076 Planarity : 0.004 0.074 2403 Dihedral : 5.703 46.513 1886 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.62 % Rotamer: Outliers : 2.58 % Allowed : 23.63 % Favored : 73.78 % 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: -2.44 (0.20), residues: 1600 helix: 0.48 (0.29), residues: 350 sheet: -2.06 (0.28), residues: 317 loop : -2.39 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 235 HIS 0.008 0.001 HIS P 268 PHE 0.028 0.001 PHE N 8 TYR 0.025 0.001 TYR K 728 ARG 0.016 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 281 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 261 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8788 (m) REVERT: K 452 CYS cc_start: 0.6819 (m) cc_final: 0.6359 (p) REVERT: K 473 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8132 (mp0) REVERT: K 530 CYS cc_start: 0.6698 (OUTLIER) cc_final: 0.6409 (m) REVERT: K 579 GLU cc_start: 0.8114 (tp30) cc_final: 0.7841 (tp30) REVERT: K 720 GLU cc_start: 0.8863 (tt0) cc_final: 0.8579 (tt0) REVERT: K 721 GLU cc_start: 0.8881 (tt0) cc_final: 0.8519 (tt0) REVERT: L 154 TYR cc_start: 0.8614 (p90) cc_final: 0.8412 (p90) REVERT: L 251 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8737 (mt) REVERT: L 276 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8548 (mm-30) REVERT: L 294 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8714 (mp) REVERT: N 20 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8264 (pt0) REVERT: N 55 ARG cc_start: 0.8299 (pmm-80) cc_final: 0.7994 (ttt180) REVERT: P 246 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8044 (tp30) REVERT: P 248 ILE cc_start: 0.8131 (mt) cc_final: 0.7757 (mm) REVERT: C 34 ARG cc_start: 0.9342 (ttm170) cc_final: 0.9044 (mmm-85) REVERT: C 50 LEU cc_start: 0.8943 (tt) cc_final: 0.8615 (mm) REVERT: C 62 GLN cc_start: 0.9250 (tp40) cc_final: 0.8991 (tm-30) REVERT: C 102 ASN cc_start: 0.7742 (m110) cc_final: 0.7246 (t0) REVERT: C 118 GLN cc_start: 0.9322 (pm20) cc_final: 0.9047 (pm20) REVERT: C 222 LYS cc_start: 0.5762 (ttpt) cc_final: 0.5378 (ptmt) outliers start: 34 outliers final: 28 residues processed: 273 average time/residue: 0.2399 time to fit residues: 95.9021 Evaluate side-chains 265 residues out of total 1483 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 233 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 530 CYS Chi-restraints excluded: chain K residue 547 CYS Chi-restraints excluded: chain K residue 661 TYR Chi-restraints excluded: chain K residue 674 VAL Chi-restraints excluded: chain K residue 684 ILE 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 149 THR Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 251 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain M residue 596 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 146 SER 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 269 VAL Chi-restraints excluded: chain N residue 300 LEU Chi-restraints excluded: chain N residue 339 ASP Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 69 HIS 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: 2.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 307 ASN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111729 restraints weight = 22274.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114713 restraints weight = 13049.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116503 restraints weight = 9729.923| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5211 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= 0.307 Angle : 0.741 12.656 18535 Z= 0.376 Chirality : 0.046 0.180 2076 Planarity : 0.005 0.071 2403 Dihedral : 5.763 39.742 1882 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.88 % Favored : 90.00 % Rotamer: Outliers : 2.96 % Allowed : 23.48 % 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 (0.21), residues: 1600 helix: 0.54 (0.29), residues: 349 sheet: -2.05 (0.28), residues: 318 loop : -2.37 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 235 HIS 0.009 0.001 HIS K 282 PHE 0.021 0.002 PHE L 147 TYR 0.023 0.002 TYR K 728 ARG 0.017 0.001 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.51 seconds wall clock time: 52 minutes 47.25 seconds (3167.25 seconds total)