Starting phenix.real_space_refine on Mon Apr 8 10:47:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5s_35992/04_2024/8j5s_35992_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.070 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 8402 2.51 5 N 2368 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 66": "OD1" <-> "OD2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 494": "OD1" <-> "OD2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 508": "OD1" <-> "OD2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "B ARG 3": "NH1" <-> "NH2" Residue "B TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ASP 217": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ARG 321": "NH1" <-> "NH2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 242": "OD1" <-> "OD2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ASP 202": "OD1" <-> "OD2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 245": "OD1" <-> "OD2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D ASP 330": "OD1" <-> "OD2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 360": "NH1" <-> "NH2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D ASP 378": "OD1" <-> "OD2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 432": "OE1" <-> "OE2" Residue "D ARG 433": "NH1" <-> "NH2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 459": "OD1" <-> "OD2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D ASP 492": "OD1" <-> "OD2" Residue "D ARG 495": "NH1" <-> "NH2" Residue "D PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 559": "OD1" <-> "OD2" Residue "D ASP 583": "OD1" <-> "OD2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "D TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D ASP 607": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13275 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4003 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 28, 'TRANS': 498} Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2475 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2130 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 13, 'TRANS': 268} Chain: "D" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4555 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 35, 'TRANS': 572} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {' MG': 2, 'ANP': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10814 SG CYS D 299 20.668 26.978 21.695 1.00 42.55 S ATOM 10947 SG CYS D 317 26.841 25.253 20.106 1.00 37.75 S ATOM 10714 SG CYS D 286 25.527 27.181 26.537 1.00 34.10 S ATOM 10761 SG CYS D 292 25.576 31.656 21.276 1.00 32.40 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLU A 510 " occ=0.94 ... (7 atoms not shown) pdb=" OE2 GLU A 510 " occ=0.94 Time building chain proxies: 7.11, per 1000 atoms: 0.54 Number of scatterers: 13275 At special positions: 0 Unit cell: (86.528, 95.68, 168.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 41 16.00 P 6 15.00 Mg 2 11.99 O 2452 8.00 N 2368 7.00 C 8402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 705 " pdb="FE4 SF4 D 705 " - pdb=" SG CYS D 292 " pdb="FE3 SF4 D 705 " - pdb=" SG CYS D 286 " pdb="FE1 SF4 D 705 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D 705 " - pdb=" SG CYS D 317 " Number of angles added : 12 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 9 sheets defined 43.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 112 through 119 removed outlier: 5.243A pdb=" N MET A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.676A pdb=" N GLN A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 317 through 324 removed outlier: 3.837A pdb=" N ALA A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.749A pdb=" N LYS A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 446 through 460 removed outlier: 3.677A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 459 " --> pdb=" O HIS A 455 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 497 through 504 removed outlier: 3.581A pdb=" N SER A 500 " --> pdb=" O PRO A 497 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 501 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR A 502 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.577A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.956A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 38 No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.781A pdb=" N ASN B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 122 removed outlier: 3.925A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 removed outlier: 3.630A pdb=" N LEU B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 162 removed outlier: 4.829A pdb=" N ARG B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.768A pdb=" N ARG B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 220 removed outlier: 3.626A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.646A pdb=" N LYS B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 3.653A pdb=" N LEU B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 254 through 272 removed outlier: 3.776A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.561A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 16 removed outlier: 4.186A pdb=" N ARG C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 37 removed outlier: 4.062A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 73 through 109 removed outlier: 3.532A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 88 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.581A pdb=" N VAL C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 138 removed outlier: 3.714A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.750A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 removed outlier: 3.738A pdb=" N SER C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 203 through 224 removed outlier: 3.994A pdb=" N ALA C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 removed outlier: 4.904A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 279 removed outlier: 4.293A pdb=" N LEU C 255 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE C 256 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Proline residue: C 257 - end of helix removed outlier: 3.702A pdb=" N LEU C 279 " --> pdb=" O ARG C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 83 through 86 No H-bonds generated for 'chain 'D' and resid 83 through 86' Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.685A pdb=" N GLU D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 116 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.709A pdb=" N ASP D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.741A pdb=" N ARG D 149 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.685A pdb=" N VAL D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 203 Processing helix chain 'D' and resid 215 through 221 removed outlier: 3.532A pdb=" N ALA D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 328 through 331 No H-bonds generated for 'chain 'D' and resid 328 through 331' Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 430 through 438 removed outlier: 3.739A pdb=" N SER D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D 438 " --> pdb=" O ARG D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 450 No H-bonds generated for 'chain 'D' and resid 447 through 450' Processing helix chain 'D' and resid 457 through 461 Processing helix chain 'D' and resid 463 through 466 No H-bonds generated for 'chain 'D' and resid 463 through 466' Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.848A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 494 Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 502 through 513 removed outlier: 3.626A pdb=" N ARG D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 509 " --> pdb=" O LYS D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 549 removed outlier: 3.591A pdb=" N ALA D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 566 removed outlier: 3.550A pdb=" N HIS D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 95 removed outlier: 7.246A pdb=" N SER A 289 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU A 93 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR A 291 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU A 95 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 293 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 264 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR A 275 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL A 262 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 141 through 146 removed outlier: 7.134A pdb=" N THR A 157 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 144 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR A 155 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 146 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 153 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 202 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= E, first strand: chain 'A' and resid 554 through 556 removed outlier: 3.684A pdb=" N PHE A 489 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR A 441 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLY A 490 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS A 463 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP A 438 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU A 465 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE A 440 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN A 467 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 62 through 64 removed outlier: 7.589A pdb=" N VAL D 12 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG D 25 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.577A pdb=" N LEU D 307 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N HIS D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 232 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL D 208 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET D 39 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE D 210 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY D 41 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY D 92 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASP D 179 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL D 94 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 577 through 582 removed outlier: 6.913A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR D 553 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 392 " --> pdb=" O TYR D 553 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE D 555 " --> pdb=" O ILE D 392 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 355 through 357 removed outlier: 3.576A pdb=" N ILE D 380 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LYS D 357 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP D 378 " --> pdb=" O LYS D 357 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1311 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: 3.65 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 5394 1.41 - 1.63: 8051 1.63 - 1.85: 70 1.85 - 2.07: 0 2.07 - 2.29: 12 Bond restraints: 13527 Sorted by residual: bond pdb=" N3B ANP D 703 " pdb=" PG ANP D 703 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" N3B ANP D 701 " pdb=" PG ANP D 701 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" O3A ANP D 701 " pdb=" PB ANP D 701 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ANP D 703 " pdb=" PB ANP D 703 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C HIS D 476 " pdb=" O HIS D 476 " ideal model delta sigma weight residual 1.236 1.295 -0.058 1.25e-02 6.40e+03 2.19e+01 ... (remaining 13522 not shown) Histogram of bond angle deviations from ideal: 72.91 - 85.20: 12 85.20 - 97.49: 1 97.49 - 109.78: 1903 109.78 - 122.07: 14133 122.07 - 134.35: 2392 Bond angle restraints: 18441 Sorted by residual: angle pdb=" N ARG D 85 " pdb=" CA ARG D 85 " pdb=" C ARG D 85 " ideal model delta sigma weight residual 114.62 106.39 8.23 1.14e+00 7.69e-01 5.21e+01 angle pdb=" N VAL D 479 " pdb=" CA VAL D 479 " pdb=" C VAL D 479 " ideal model delta sigma weight residual 111.05 104.26 6.79 1.25e+00 6.40e-01 2.95e+01 angle pdb=" N ARG B 40 " pdb=" CA ARG B 40 " pdb=" C ARG B 40 " ideal model delta sigma weight residual 109.59 101.43 8.16 1.61e+00 3.86e-01 2.57e+01 angle pdb=" C MET A 589 " pdb=" N ARG A 590 " pdb=" CA ARG A 590 " ideal model delta sigma weight residual 122.41 115.60 6.81 1.41e+00 5.03e-01 2.34e+01 angle pdb=" CA TRP A 281 " pdb=" CB TRP A 281 " pdb=" CG TRP A 281 " ideal model delta sigma weight residual 113.60 122.37 -8.77 1.90e+00 2.77e-01 2.13e+01 ... (remaining 18436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7080 17.97 - 35.95: 801 35.95 - 53.92: 178 53.92 - 71.90: 36 71.90 - 89.87: 18 Dihedral angle restraints: 8113 sinusoidal: 3140 harmonic: 4973 Sorted by residual: dihedral pdb=" CA ARG B 123 " pdb=" C ARG B 123 " pdb=" N GLN B 124 " pdb=" CA GLN B 124 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ALA A 150 " pdb=" C ALA A 150 " pdb=" N PRO A 151 " pdb=" CA PRO A 151 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE A 322 " pdb=" C ILE A 322 " pdb=" N ALA A 323 " pdb=" CA ALA A 323 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1768 0.067 - 0.134: 372 0.134 - 0.201: 29 0.201 - 0.268: 4 0.268 - 0.335: 2 Chirality restraints: 2175 Sorted by residual: chirality pdb=" C3' ANP D 703 " pdb=" C2' ANP D 703 " pdb=" C4' ANP D 703 " pdb=" O3' ANP D 703 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' ANP D 701 " pdb=" C2' ANP D 701 " pdb=" C4' ANP D 701 " pdb=" O3' ANP D 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA CYS D 292 " pdb=" N CYS D 292 " pdb=" C CYS D 292 " pdb=" CB CYS D 292 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2172 not shown) Planarity restraints: 2379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 43 " -0.585 9.50e-02 1.11e+02 2.62e-01 4.20e+01 pdb=" NE ARG B 43 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 43 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 43 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 43 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 40 " -0.347 9.50e-02 1.11e+02 1.56e-01 1.48e+01 pdb=" NE ARG B 40 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 40 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 40 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 40 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.024 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP A 281 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.001 2.00e-02 2.50e+03 ... (remaining 2376 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1606 2.74 - 3.28: 13200 3.28 - 3.82: 21513 3.82 - 4.36: 27024 4.36 - 4.90: 45978 Nonbonded interactions: 109321 Sorted by model distance: nonbonded pdb=" OG SER A 423 " pdb=" OE1 GLU A 428 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP A 416 " pdb=" NH2 ARG A 427 " model vdw 2.202 2.520 nonbonded pdb=" OG1 THR A 147 " pdb=" O VAL A 153 " model vdw 2.203 2.440 nonbonded pdb=" NH1 ARG D 375 " pdb=" OD1 ASP D 378 " model vdw 2.214 2.520 nonbonded pdb=" OD1 ASP A 208 " pdb=" OD1 ASP A 209 " model vdw 2.232 3.040 ... (remaining 109316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.94 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: 2.860 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: 7.650 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.009 0.162 13527 Z= 0.592 Angle : 0.852 10.380 18441 Z= 0.491 Chirality : 0.054 0.335 2175 Planarity : 0.008 0.262 2379 Dihedral : 16.458 89.871 4923 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.36 % Allowed : 0.80 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.19), residues: 1734 helix: -0.61 (0.18), residues: 816 sheet: -2.16 (0.40), residues: 148 loop : -2.45 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 281 HIS 0.010 0.002 HIS D 568 PHE 0.028 0.002 PHE C 224 TYR 0.017 0.002 TYR A 340 ARG 0.009 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.503 Fit side-chains REVERT: C 273 ASP cc_start: 0.7986 (m-30) cc_final: 0.7786 (m-30) REVERT: C 280 ASP cc_start: 0.7127 (m-30) cc_final: 0.6893 (m-30) outliers start: 5 outliers final: 3 residues processed: 175 average time/residue: 1.3036 time to fit residues: 248.8934 Evaluate side-chains 140 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 43 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 GLN B 275 HIS ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13527 Z= 0.191 Angle : 0.603 12.134 18441 Z= 0.307 Chirality : 0.043 0.156 2175 Planarity : 0.005 0.064 2379 Dihedral : 7.771 55.777 1989 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.33 % Allowed : 11.29 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.80 (0.19), residues: 1734 helix: -0.19 (0.19), residues: 796 sheet: -1.96 (0.39), residues: 161 loop : -2.08 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 172 HIS 0.006 0.001 HIS D 568 PHE 0.016 0.001 PHE C 256 TYR 0.017 0.001 TYR A 340 ARG 0.007 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.514 Fit side-chains REVERT: A 589 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5764 (pmt) REVERT: C 46 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5633 (t80) REVERT: D 161 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.7887 (tp40) outliers start: 32 outliers final: 10 residues processed: 164 average time/residue: 1.2057 time to fit residues: 217.9405 Evaluate side-chains 148 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 439 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 319 GLN ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13527 Z= 0.260 Angle : 0.603 8.329 18441 Z= 0.308 Chirality : 0.044 0.156 2175 Planarity : 0.005 0.065 2379 Dihedral : 6.303 43.686 1979 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.91 % Allowed : 15.66 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.20), residues: 1734 helix: -0.14 (0.19), residues: 810 sheet: -2.10 (0.37), residues: 175 loop : -1.97 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 172 HIS 0.006 0.001 HIS B 72 PHE 0.015 0.001 PHE C 256 TYR 0.016 0.001 TYR A 340 ARG 0.014 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.511 Fit side-chains REVERT: A 79 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 589 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5839 (pmm) REVERT: B 222 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (p0) REVERT: C 46 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.5679 (t80) REVERT: D 161 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: D 483 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8478 (pt) REVERT: D 551 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8440 (mp) outliers start: 40 outliers final: 16 residues processed: 167 average time/residue: 1.1281 time to fit residues: 208.7546 Evaluate side-chains 153 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 551 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13527 Z= 0.238 Angle : 0.582 14.124 18441 Z= 0.293 Chirality : 0.043 0.153 2175 Planarity : 0.005 0.065 2379 Dihedral : 5.620 50.181 1979 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 17.41 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.20), residues: 1734 helix: -0.10 (0.19), residues: 810 sheet: -1.94 (0.37), residues: 175 loop : -1.93 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 172 HIS 0.005 0.001 HIS B 72 PHE 0.013 0.001 PHE C 256 TYR 0.014 0.001 TYR A 340 ARG 0.006 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 1.519 Fit side-chains REVERT: A 589 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5909 (pmm) REVERT: B 222 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8151 (p0) REVERT: C 46 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.5684 (t80) REVERT: D 161 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7924 (tp40) REVERT: D 483 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8571 (pt) REVERT: D 551 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8641 (mp) outliers start: 41 outliers final: 19 residues processed: 167 average time/residue: 1.1435 time to fit residues: 210.8874 Evaluate side-chains 155 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 551 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13527 Z= 0.461 Angle : 0.686 10.998 18441 Z= 0.348 Chirality : 0.048 0.163 2175 Planarity : 0.005 0.066 2379 Dihedral : 5.953 57.602 1979 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.52 % Allowed : 18.21 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.19), residues: 1734 helix: -0.32 (0.18), residues: 806 sheet: -1.87 (0.38), residues: 175 loop : -2.10 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 172 HIS 0.009 0.001 HIS B 72 PHE 0.015 0.002 PHE C 256 TYR 0.017 0.002 TYR B 169 ARG 0.008 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 136 time to evaluate : 1.483 Fit side-chains REVERT: B 35 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: C 46 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6040 (t80) REVERT: C 115 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6301 (ttp-170) REVERT: D 161 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.7974 (tp40) REVERT: D 483 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8654 (pt) REVERT: D 605 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7482 (mt0) outliers start: 62 outliers final: 36 residues processed: 176 average time/residue: 1.1405 time to fit residues: 222.4583 Evaluate side-chains 171 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 129 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 605 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.3980 chunk 149 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 87 optimal weight: 0.2980 chunk 160 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13527 Z= 0.159 Angle : 0.559 10.236 18441 Z= 0.286 Chirality : 0.042 0.186 2175 Planarity : 0.005 0.065 2379 Dihedral : 5.453 54.326 1979 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.28 % Allowed : 20.10 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.51 (0.20), residues: 1734 helix: 0.02 (0.19), residues: 801 sheet: -1.73 (0.37), residues: 183 loop : -1.90 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 172 HIS 0.003 0.001 HIS D 568 PHE 0.015 0.001 PHE C 256 TYR 0.010 0.001 TYR A 340 ARG 0.008 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.438 Fit side-chains REVERT: B 129 ASP cc_start: 0.7391 (t0) cc_final: 0.7170 (t0) REVERT: C 46 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.5748 (t80) REVERT: C 163 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7434 (mtt90) REVERT: D 161 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7893 (tp40) REVERT: D 483 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8613 (pt) REVERT: D 574 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8402 (tp) outliers start: 45 outliers final: 23 residues processed: 171 average time/residue: 1.1301 time to fit residues: 213.9237 Evaluate side-chains 159 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13527 Z= 0.198 Angle : 0.577 14.669 18441 Z= 0.291 Chirality : 0.042 0.178 2175 Planarity : 0.005 0.065 2379 Dihedral : 5.323 54.655 1979 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.13 % Allowed : 21.41 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.39 (0.20), residues: 1734 helix: 0.10 (0.19), residues: 801 sheet: -1.68 (0.37), residues: 183 loop : -1.82 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 172 HIS 0.004 0.001 HIS B 72 PHE 0.015 0.001 PHE C 256 TYR 0.011 0.001 TYR A 340 ARG 0.014 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 137 time to evaluate : 1.353 Fit side-chains REVERT: B 35 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: C 46 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5779 (t80) REVERT: C 163 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7405 (mtt90) REVERT: C 168 MET cc_start: 0.7387 (ppp) cc_final: 0.7113 (ptt) REVERT: D 161 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.7898 (tp40) REVERT: D 483 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8610 (pt) REVERT: D 551 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8749 (mp) outliers start: 43 outliers final: 27 residues processed: 168 average time/residue: 1.1608 time to fit residues: 215.1053 Evaluate side-chains 162 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 161 GLN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 0.0070 chunk 144 optimal weight: 6.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13527 Z= 0.153 Angle : 0.553 14.455 18441 Z= 0.280 Chirality : 0.041 0.184 2175 Planarity : 0.005 0.064 2379 Dihedral : 5.067 52.135 1979 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.91 % Allowed : 21.92 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.20), residues: 1734 helix: 0.27 (0.19), residues: 802 sheet: -1.33 (0.38), residues: 176 loop : -1.66 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 172 HIS 0.003 0.000 HIS D 568 PHE 0.011 0.001 PHE C 256 TYR 0.010 0.001 TYR A 340 ARG 0.014 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.456 Fit side-chains REVERT: B 167 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8401 (p90) REVERT: C 46 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.5506 (t80) REVERT: D 483 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8609 (pt) REVERT: D 551 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8728 (mp) outliers start: 40 outliers final: 25 residues processed: 173 average time/residue: 1.2271 time to fit residues: 233.0679 Evaluate side-chains 159 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 0.0040 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 0.0470 chunk 146 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13527 Z= 0.150 Angle : 0.554 13.337 18441 Z= 0.280 Chirality : 0.041 0.148 2175 Planarity : 0.005 0.064 2379 Dihedral : 4.959 51.359 1979 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.62 % Allowed : 22.58 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1734 helix: 0.36 (0.19), residues: 803 sheet: -1.48 (0.37), residues: 188 loop : -1.55 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 172 HIS 0.002 0.000 HIS D 568 PHE 0.010 0.001 PHE C 256 TYR 0.009 0.001 TYR A 340 ARG 0.016 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: C 46 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5439 (t80) REVERT: D 483 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8580 (pt) REVERT: D 551 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8722 (mp) outliers start: 36 outliers final: 29 residues processed: 162 average time/residue: 1.2187 time to fit residues: 217.4778 Evaluate side-chains 159 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13527 Z= 0.231 Angle : 0.576 14.504 18441 Z= 0.291 Chirality : 0.042 0.147 2175 Planarity : 0.005 0.064 2379 Dihedral : 5.023 54.155 1979 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.55 % Allowed : 22.87 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.20), residues: 1734 helix: 0.36 (0.19), residues: 803 sheet: -1.45 (0.37), residues: 183 loop : -1.63 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 172 HIS 0.003 0.001 HIS D 119 PHE 0.014 0.001 PHE C 256 TYR 0.012 0.001 TYR A 340 ARG 0.017 0.000 ARG A 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: C 46 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.5543 (t80) REVERT: C 168 MET cc_start: 0.7344 (ppp) cc_final: 0.7042 (ptt) REVERT: D 388 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7571 (mtt-85) REVERT: D 483 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8598 (pt) REVERT: D 551 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8768 (mp) outliers start: 35 outliers final: 28 residues processed: 156 average time/residue: 1.2300 time to fit residues: 210.7701 Evaluate side-chains 161 residues out of total 1373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 388 ARG Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096802 restraints weight = 19874.681| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.69 r_work: 0.3022 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13527 Z= 0.250 Angle : 0.597 12.192 18441 Z= 0.303 Chirality : 0.043 0.153 2175 Planarity : 0.005 0.064 2379 Dihedral : 5.172 56.175 1979 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.69 % Allowed : 22.80 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.20), residues: 1734 helix: 0.32 (0.19), residues: 805 sheet: -1.22 (0.39), residues: 173 loop : -1.75 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 172 HIS 0.003 0.001 HIS D 119 PHE 0.017 0.001 PHE C 256 TYR 0.013 0.001 TYR A 340 ARG 0.015 0.000 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4356.88 seconds wall clock time: 78 minutes 45.53 seconds (4725.53 seconds total)