Starting phenix.real_space_refine on Fri Feb 16 06:32:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lbg_23254/02_2024/7lbg_23254.pdb" } resolution = 2.6 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= -0.027 sd= 0.763 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 65 5.16 5 C 9289 2.51 5 N 2453 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14586 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5118 Classifications: {'peptide': 635} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 602} Chain breaks: 6 Chain: "B" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2462 Classifications: {'peptide': 296} Link IDs: {'PCIS': 3, 'PTRANS': 14, 'TRANS': 278} Chain breaks: 3 Chain: "D" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1235 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1005 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.07, per 1000 atoms: 0.55 Number of scatterers: 14586 At special positions: 0 Unit cell: (96.7788, 174.441, 163.688, 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 65 16.00 O 2779 8.00 N 2453 7.00 C 9289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.02 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 6 " - " MAN J 7 " ALPHA1-6 " BMA J 3 " - " MAN J 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 67 " " NAG A 803 " - " ASN A 62 " " NAG A 804 " - " ASN A 55 " " NAG A 805 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 85 " " NAG C 602 " - " ASN C 101 " " NAG C 603 " - " ASN C 155 " " NAG C 604 " - " ASN C 217 " " NAG C 605 " - " ASN C 240 " " NAG C 606 " - " ASN C 348 " " NAG C 607 " - " ASN C 365 " " NAG C 608 " - " ASN C 383 " " NAG C 609 " - " ASN C 452 " " NAG C 610 " - " ASN C 128 " " NAG C 611 " - " ASN C 169 " " NAG J 1 " - " ASN C 160 " Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 27 sheets defined 29.4% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.710A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 285 through 294 removed outlier: 4.221A pdb=" N SER A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR A 291 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.586A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.709A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.816A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.598A pdb=" N LEU A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 removed outlier: 3.788A pdb=" N VAL A 710 " --> pdb=" O THR A 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.575A pdb=" N LEU B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.835A pdb=" N LEU B 167 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.974A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 252 removed outlier: 3.952A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 214 removed outlier: 3.640A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.555A pdb=" N ARG C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.741A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 413 through 435 Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.555A pdb=" N LEU C 456 " --> pdb=" O ASN C 452 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.829A pdb=" N GLY D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.525A pdb=" N VAL E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.555A pdb=" N GLN F 88 " --> pdb=" O GLN F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.884A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.220A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 88 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 81 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 90 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN A 79 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET A 92 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A 77 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS B 177 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 192 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 181 " --> pdb=" O ASN B 190 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 190 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 183 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 188 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.797A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.647A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP A 658 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N VAL A 663 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.507A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.328A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.675A pdb=" N TYR C 124 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N TYR C 122 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 117 through 118 removed outlier: 6.632A pdb=" N VAL D 83 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LYS D 115 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU D 85 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 88 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.838A pdb=" N THR C 192 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.334A pdb=" N GLU D 63 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU D 103 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS D 65 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASN D 105 " --> pdb=" O HIS D 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU D 67 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 100 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU D 128 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE D 102 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.524A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AC2, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.600A pdb=" N ARG F 61 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TRP F 70 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.928A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 27 through 30 Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.939A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY G 112 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR G 125 " --> pdb=" O GLN G 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.013A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 34 through 35 removed outlier: 3.874A pdb=" N VAL H 142 " --> pdb=" O ARG H 121 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1509 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: 5.21 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4621 1.34 - 1.46: 3656 1.46 - 1.58: 6549 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 14923 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C1 MAN J 7 " pdb=" C2 MAN J 7 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 NAG C 610 " pdb=" O5 NAG C 610 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN J 5 " pdb=" C2 MAN J 5 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.64e+00 ... (remaining 14918 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.92: 508 106.92 - 113.71: 8411 113.71 - 120.50: 5487 120.50 - 127.29: 5707 127.29 - 134.08: 177 Bond angle restraints: 20290 Sorted by residual: angle pdb=" CB LYS B 64 " pdb=" CG LYS B 64 " pdb=" CD LYS B 64 " ideal model delta sigma weight residual 111.30 116.61 -5.31 2.30e+00 1.89e-01 5.32e+00 angle pdb=" CA ASN C 101 " pdb=" CB ASN C 101 " pdb=" CG ASN C 101 " ideal model delta sigma weight residual 112.60 114.88 -2.28 1.00e+00 1.00e+00 5.19e+00 angle pdb=" C3 MAN J 4 " pdb=" C2 MAN J 4 " pdb=" O2 MAN J 4 " ideal model delta sigma weight residual 111.77 104.94 6.83 3.00e+00 1.11e-01 5.19e+00 angle pdb=" C ASN A 85 " pdb=" CA ASN A 85 " pdb=" CB ASN A 85 " ideal model delta sigma weight residual 111.80 108.48 3.32 1.46e+00 4.69e-01 5.16e+00 angle pdb=" C3 MAN J 6 " pdb=" C2 MAN J 6 " pdb=" O2 MAN J 6 " ideal model delta sigma weight residual 111.77 105.24 6.53 3.00e+00 1.11e-01 4.74e+00 ... (remaining 20285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 8839 22.35 - 44.70: 331 44.70 - 67.04: 59 67.04 - 89.39: 27 89.39 - 111.74: 4 Dihedral angle restraints: 9260 sinusoidal: 4007 harmonic: 5253 Sorted by residual: dihedral pdb=" CB CYS D 52 " pdb=" SG CYS D 52 " pdb=" SG CYS D 197 " pdb=" CB CYS D 197 " ideal model delta sinusoidal sigma weight residual -86.00 -167.27 81.27 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CA PRO C 145 " pdb=" C PRO C 145 " pdb=" N SER C 146 " pdb=" CA SER C 146 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ALA B 194 " pdb=" C ALA B 194 " pdb=" N ILE B 195 " pdb=" CA ILE B 195 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2011 0.053 - 0.105: 278 0.105 - 0.158: 86 0.158 - 0.210: 1 0.210 - 0.263: 3 Chirality restraints: 2379 Sorted by residual: chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C 611 " pdb=" ND2 ASN C 169 " pdb=" C2 NAG C 611 " pdb=" O5 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN C 101 " pdb=" N ASN C 101 " pdb=" C ASN C 101 " pdb=" CB ASN C 101 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2376 not shown) Planarity restraints: 2560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 344 " 0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 345 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 345 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 345 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 94 " 0.236 9.50e-02 1.11e+02 1.06e-01 7.47e+00 pdb=" NE ARG A 94 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 94 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 94 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 94 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 253 " -0.229 9.50e-02 1.11e+02 1.03e-01 7.25e+00 pdb=" NE ARG C 253 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG C 253 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 253 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 253 " -0.003 2.00e-02 2.50e+03 ... (remaining 2557 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 189 2.65 - 3.21: 13461 3.21 - 3.77: 22227 3.77 - 4.34: 33742 4.34 - 4.90: 53996 Nonbonded interactions: 123615 Sorted by model distance: nonbonded pdb=" NH2 ARG A 365 " pdb=" OD2 ASP A 368 " model vdw 2.085 2.520 nonbonded pdb=" ND1 HIS C 360 " pdb=" O LEU C 459 " model vdw 2.192 2.520 nonbonded pdb=" O LEU G 34 " pdb=" N GLU G 133 " model vdw 2.209 2.520 nonbonded pdb=" OG SER B 83 " pdb=" OE1 GLU B 176 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP E 128 " pdb=" N ILE E 129 " model vdw 2.283 2.520 ... (remaining 123610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.300 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.270 Find NCS groups from input model: 0.380 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.003 0.057 14923 Z= 0.217 Angle : 0.580 6.937 20290 Z= 0.282 Chirality : 0.043 0.263 2379 Planarity : 0.006 0.106 2542 Dihedral : 12.952 111.738 5827 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1750 helix: 0.45 (0.25), residues: 402 sheet: 0.37 (0.24), residues: 432 loop : 0.34 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 460 HIS 0.005 0.001 HIS A 187 PHE 0.027 0.002 PHE H 52 TYR 0.020 0.002 TYR A 344 ARG 0.015 0.002 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 317 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7694 (mmtm) REVERT: D 96 HIS cc_start: 0.7843 (t70) cc_final: 0.7576 (t70) REVERT: D 115 LYS cc_start: 0.7382 (mmpt) cc_final: 0.6495 (pttp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 1.4667 time to fit residues: 450.8342 Evaluate side-chains 217 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 480 HIS B 203 ASN C 215 GLN D 155 HIS D 157 ASN D 202 ASN D 207 ASN E 26 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14923 Z= 0.221 Angle : 0.579 6.827 20290 Z= 0.296 Chirality : 0.044 0.236 2379 Planarity : 0.004 0.060 2542 Dihedral : 7.773 80.464 2490 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 8.68 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1750 helix: 1.43 (0.25), residues: 405 sheet: 0.54 (0.24), residues: 422 loop : 0.47 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 460 HIS 0.005 0.001 HIS B 236 PHE 0.030 0.002 PHE H 52 TYR 0.026 0.002 TYR A 84 ARG 0.007 0.001 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 GLN cc_start: 0.7687 (pm20) cc_final: 0.7429 (pm20) REVERT: C 132 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6862 (mttp) REVERT: C 317 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7611 (mmtm) REVERT: F 112 GLU cc_start: 0.7662 (mp0) cc_final: 0.7360 (mp0) REVERT: H 96 ASP cc_start: 0.7894 (t70) cc_final: 0.7337 (t70) outliers start: 28 outliers final: 10 residues processed: 243 average time/residue: 1.4312 time to fit residues: 378.7956 Evaluate side-chains 231 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 127 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS E 53 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14923 Z= 0.324 Angle : 0.595 7.234 20290 Z= 0.303 Chirality : 0.045 0.237 2379 Planarity : 0.005 0.048 2542 Dihedral : 7.440 72.621 2490 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.14 % Allowed : 10.75 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1750 helix: 1.41 (0.25), residues: 411 sheet: 0.36 (0.24), residues: 433 loop : 0.32 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 438 HIS 0.008 0.001 HIS B 236 PHE 0.029 0.002 PHE H 52 TYR 0.016 0.002 TYR C 188 ARG 0.011 0.001 ARG C 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: A 168 MET cc_start: 0.8039 (mpt) cc_final: 0.7642 (mmt) REVERT: C 132 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7048 (mttp) REVERT: C 317 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7634 (mmpt) REVERT: C 375 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8119 (mp) REVERT: D 115 LYS cc_start: 0.7105 (mmpt) cc_final: 0.6020 (pttp) REVERT: D 116 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7195 (m) REVERT: F 112 GLU cc_start: 0.7695 (mp0) cc_final: 0.7436 (mp0) REVERT: F 130 ASP cc_start: 0.8424 (m-30) cc_final: 0.8202 (m-30) REVERT: G 89 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7131 (mtm110) outliers start: 34 outliers final: 15 residues processed: 248 average time/residue: 1.4048 time to fit residues: 379.4628 Evaluate side-chains 236 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 216 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 83 optimal weight: 0.0270 chunk 151 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS D 207 ASN G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14923 Z= 0.177 Angle : 0.518 6.493 20290 Z= 0.265 Chirality : 0.042 0.228 2379 Planarity : 0.004 0.044 2542 Dihedral : 6.937 62.485 2490 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 11.13 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1750 helix: 1.79 (0.26), residues: 405 sheet: 0.50 (0.25), residues: 427 loop : 0.41 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 438 HIS 0.003 0.001 HIS B 236 PHE 0.016 0.001 PHE H 52 TYR 0.012 0.001 TYR C 188 ARG 0.004 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8041 (mpt) cc_final: 0.7644 (mmt) REVERT: A 255 ARG cc_start: 0.8109 (mtp-110) cc_final: 0.7902 (mtp85) REVERT: B 63 ASP cc_start: 0.8419 (p0) cc_final: 0.8138 (p0) REVERT: C 126 GLN cc_start: 0.8441 (pt0) cc_final: 0.8018 (pt0) REVERT: C 317 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7660 (mptt) REVERT: D 115 LYS cc_start: 0.7076 (mmpt) cc_final: 0.6045 (pttp) REVERT: D 116 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7181 (m) REVERT: F 124 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7836 (mtt90) REVERT: F 130 ASP cc_start: 0.8323 (m-30) cc_final: 0.8120 (m-30) REVERT: G 89 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7084 (mtm110) outliers start: 34 outliers final: 13 residues processed: 246 average time/residue: 1.4025 time to fit residues: 377.6068 Evaluate side-chains 235 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 0.0000 chunk 151 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS E 53 ASN G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14923 Z= 0.291 Angle : 0.570 7.358 20290 Z= 0.290 Chirality : 0.044 0.229 2379 Planarity : 0.004 0.041 2542 Dihedral : 6.883 59.189 2490 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.89 % Allowed : 11.82 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1750 helix: 1.71 (0.26), residues: 405 sheet: 0.33 (0.24), residues: 438 loop : 0.37 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 438 HIS 0.007 0.001 HIS B 236 PHE 0.022 0.002 PHE H 52 TYR 0.014 0.002 TYR C 188 ARG 0.003 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8087 (mpt) cc_final: 0.7657 (mmt) REVERT: A 209 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 126 GLN cc_start: 0.8434 (pt0) cc_final: 0.8045 (pt0) REVERT: C 317 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7655 (mmtm) REVERT: C 375 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8074 (mp) REVERT: D 115 LYS cc_start: 0.6871 (mmpt) cc_final: 0.5848 (pttp) REVERT: D 116 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7283 (m) REVERT: F 124 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7838 (mtt90) REVERT: F 130 ASP cc_start: 0.8399 (m-30) cc_final: 0.8159 (m-30) REVERT: G 89 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7245 (mtm110) outliers start: 46 outliers final: 20 residues processed: 253 average time/residue: 1.4404 time to fit residues: 396.5559 Evaluate side-chains 247 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 108 HIS D 155 HIS G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14923 Z= 0.198 Angle : 0.523 6.834 20290 Z= 0.267 Chirality : 0.042 0.220 2379 Planarity : 0.004 0.039 2542 Dihedral : 6.601 59.425 2490 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.33 % Allowed : 13.14 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1750 helix: 1.85 (0.26), residues: 405 sheet: 0.40 (0.24), residues: 435 loop : 0.39 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 438 HIS 0.005 0.001 HIS A 213 PHE 0.014 0.001 PHE A 379 TYR 0.012 0.001 TYR H 118 ARG 0.003 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: A 168 MET cc_start: 0.8092 (mpt) cc_final: 0.7679 (mmt) REVERT: C 126 GLN cc_start: 0.8412 (pt0) cc_final: 0.7991 (pt0) REVERT: C 317 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7644 (mmtm) REVERT: C 375 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8053 (mp) REVERT: D 115 LYS cc_start: 0.6809 (mmpt) cc_final: 0.5809 (pttp) REVERT: D 116 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7274 (m) REVERT: E 126 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8184 (mtpp) REVERT: G 89 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7170 (mtm110) outliers start: 37 outliers final: 21 residues processed: 244 average time/residue: 1.4069 time to fit residues: 373.9784 Evaluate side-chains 245 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 108 HIS D 155 HIS E 53 ASN G 73 GLN G 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14923 Z= 0.267 Angle : 0.554 7.373 20290 Z= 0.282 Chirality : 0.043 0.218 2379 Planarity : 0.004 0.039 2542 Dihedral : 6.621 59.584 2490 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.77 % Allowed : 13.14 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1750 helix: 1.80 (0.26), residues: 405 sheet: 0.35 (0.24), residues: 435 loop : 0.35 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 438 HIS 0.006 0.001 HIS B 236 PHE 0.016 0.002 PHE H 52 TYR 0.012 0.002 TYR C 188 ARG 0.003 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: A 168 MET cc_start: 0.8095 (mpt) cc_final: 0.7654 (mmt) REVERT: C 126 GLN cc_start: 0.8387 (pt0) cc_final: 0.7946 (pt0) REVERT: C 317 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7649 (mmtm) REVERT: C 375 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8064 (mp) REVERT: D 115 LYS cc_start: 0.6874 (mmpt) cc_final: 0.5950 (pttp) REVERT: D 116 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7281 (m) REVERT: D 149 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: E 126 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8105 (mtpp) REVERT: G 89 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7211 (mtm110) REVERT: G 121 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8487 (mt0) outliers start: 44 outliers final: 26 residues processed: 241 average time/residue: 1.3943 time to fit residues: 368.4630 Evaluate side-chains 247 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 121 GLN Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 83 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 108 HIS D 155 HIS G 29 GLN G 73 GLN G 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14923 Z= 0.193 Angle : 0.525 6.955 20290 Z= 0.268 Chirality : 0.042 0.203 2379 Planarity : 0.004 0.038 2542 Dihedral : 6.441 59.369 2490 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.52 % Allowed : 13.71 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.20), residues: 1750 helix: 1.90 (0.26), residues: 405 sheet: 0.39 (0.24), residues: 435 loop : 0.41 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 438 HIS 0.004 0.001 HIS B 236 PHE 0.013 0.001 PHE A 379 TYR 0.012 0.001 TYR H 118 ARG 0.003 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 219 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: A 168 MET cc_start: 0.8107 (mpt) cc_final: 0.7674 (mmt) REVERT: A 255 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7887 (mtp85) REVERT: C 126 GLN cc_start: 0.8404 (pt0) cc_final: 0.7991 (pt0) REVERT: C 317 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7645 (mmtm) REVERT: C 375 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8046 (mp) REVERT: D 115 LYS cc_start: 0.6856 (mmpt) cc_final: 0.5912 (pttp) REVERT: D 116 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7211 (m) REVERT: D 149 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: E 126 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8181 (mtpp) REVERT: G 89 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7222 (mtm110) outliers start: 40 outliers final: 25 residues processed: 239 average time/residue: 1.4297 time to fit residues: 372.6720 Evaluate side-chains 246 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS E 102 GLN G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14923 Z= 0.216 Angle : 0.540 9.989 20290 Z= 0.273 Chirality : 0.042 0.209 2379 Planarity : 0.004 0.038 2542 Dihedral : 6.400 59.551 2490 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.33 % Allowed : 13.65 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1750 helix: 1.86 (0.26), residues: 405 sheet: 0.36 (0.24), residues: 437 loop : 0.39 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 438 HIS 0.005 0.001 HIS B 236 PHE 0.014 0.002 PHE A 379 TYR 0.011 0.001 TYR H 118 ARG 0.003 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 218 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: A 168 MET cc_start: 0.8118 (mpt) cc_final: 0.7673 (mmt) REVERT: A 255 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7909 (mtp85) REVERT: C 126 GLN cc_start: 0.8366 (pt0) cc_final: 0.7943 (pt0) REVERT: C 317 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7656 (mmtm) REVERT: C 375 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8047 (mp) REVERT: D 115 LYS cc_start: 0.6841 (mmpt) cc_final: 0.5875 (pttp) REVERT: D 116 THR cc_start: 0.7562 (OUTLIER) cc_final: 0.7229 (m) REVERT: D 149 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7064 (mm-30) REVERT: E 126 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8104 (mtpp) REVERT: G 89 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7300 (mtm110) REVERT: G 121 GLN cc_start: 0.8738 (mt0) cc_final: 0.8520 (mt0) outliers start: 37 outliers final: 27 residues processed: 236 average time/residue: 1.4698 time to fit residues: 378.0948 Evaluate side-chains 244 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS E 53 ASN G 73 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14923 Z= 0.301 Angle : 0.590 10.163 20290 Z= 0.298 Chirality : 0.044 0.216 2379 Planarity : 0.004 0.039 2542 Dihedral : 6.572 59.634 2490 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.20 % Allowed : 14.03 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1750 helix: 1.69 (0.26), residues: 405 sheet: 0.24 (0.24), residues: 440 loop : 0.30 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 438 HIS 0.007 0.001 HIS B 236 PHE 0.016 0.002 PHE B 105 TYR 0.013 0.002 TYR C 188 ARG 0.004 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3500 Ramachandran restraints generated. 1750 Oldfield, 0 Emsley, 1750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: A 168 MET cc_start: 0.8132 (mpt) cc_final: 0.7670 (mmt) REVERT: C 126 GLN cc_start: 0.8390 (pt0) cc_final: 0.7991 (pt0) REVERT: C 317 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7690 (mmtm) REVERT: D 115 LYS cc_start: 0.6785 (mmpt) cc_final: 0.5866 (pttp) REVERT: D 116 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7254 (m) REVERT: D 149 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7087 (mm-30) REVERT: E 126 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: G 89 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7224 (mtm110) outliers start: 35 outliers final: 25 residues processed: 235 average time/residue: 1.4557 time to fit residues: 372.2528 Evaluate side-chains 249 residues out of total 1591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 598 LYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 165 ARG Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 126 LYS Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 129 SER Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 128 optimal weight: 0.0010 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 155 HIS G 81 ASN G 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091606 restraints weight = 19853.661| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.84 r_work: 0.2904 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14923 Z= 0.219 Angle : 0.559 13.451 20290 Z= 0.281 Chirality : 0.043 0.218 2379 Planarity : 0.004 0.038 2542 Dihedral : 6.433 59.866 2490 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.08 % Allowed : 14.47 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1750 helix: 1.81 (0.26), residues: 405 sheet: 0.27 (0.24), residues: 440 loop : 0.32 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 438 HIS 0.004 0.001 HIS B 236 PHE 0.014 0.002 PHE A 379 TYR 0.012 0.001 TYR H 118 ARG 0.004 0.000 ARG B 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.46 seconds wall clock time: 113 minutes 35.29 seconds (6815.29 seconds total)