Starting phenix.real_space_refine on Fri Jul 3 19:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lbf_23253/07_2026/7lbf_23253.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.033 sd= 0.674 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 9955 2.51 5 N 2596 2.21 5 O 3031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15656 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5203 Classifications: {'peptide': 647} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 614} Chain breaks: 4 Chain: "B" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1860 Classifications: {'peptide': 236} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 216} Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2484 Classifications: {'peptide': 299} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 280} Chain breaks: 3 Chain: "D" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2142 Classifications: {'peptide': 274} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 258} Chain breaks: 3 Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 927 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1001 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.17, per 1000 atoms: 0.20 Number of scatterers: 15656 At special positions: 0 Unit cell: (95.9494, 177.033, 167.574, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 3031 8.00 N 2596 7.00 C 9955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS B 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 624 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS C 149 " distance=2.04 Simple disulfide: pdb=" SG CYS C 167 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 111 " distance=2.03 Simple disulfide: pdb=" SG CYS F 45 " - pdb=" SG CYS F 119 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 804 " - " ASN A 700 " " NAG B 301 " - " ASN B 74 " " NAG C 601 " - " ASN C 85 " " NAG C 603 " - " ASN C 155 " " NAG C 604 " - " ASN C 217 " " NAG C 605 " - " ASN C 240 " " NAG C 606 " - " ASN C 365 " " NAG C 608 " - " ASN C 452 " " NAG D 601 " - " ASN D 103 " " NAG D 602 " - " ASN D 179 " " NAG I 1 " - " ASN C 348 " " NAG J 1 " - " ASN C 431 " " NAG K 1 " - " ASN C 160 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 672.0 milliseconds 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3650 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 34 sheets defined 27.4% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.602A pdb=" N PHE A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.668A pdb=" N TYR A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.843A pdb=" N GLY A 358 " --> pdb=" O GLN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 385 Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.741A pdb=" N LEU A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 436 through 454 removed outlier: 3.620A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.664A pdb=" N HIS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.761A pdb=" N CYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.674A pdb=" N LEU A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 644 through 648 Processing helix chain 'A' and resid 671 through 680 Processing helix chain 'A' and resid 681 through 684 Processing helix chain 'A' and resid 707 through 710 Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.509A pdb=" N THR B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 236 removed outlier: 3.874A pdb=" N PHE B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 253 removed outlier: 4.147A pdb=" N ARG B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 198 through 215 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 240 through 251 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 336 through 343 removed outlier: 6.479A pdb=" N GLU C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 361 through 364 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 413 through 436 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.661A pdb=" N SER C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'F' and resid 51 through 55 removed outlier: 3.901A pdb=" N TYR F 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 114 Processing helix chain 'G' and resid 107 through 111 removed outlier: 4.087A pdb=" N VAL G 111 " --> pdb=" O THR G 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 114 removed outlier: 3.669A pdb=" N THR H 114 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.145A pdb=" N SER A 64 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER A 77 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 183 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASN A 79 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 178 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 194 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 180 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE B 189 " --> pdb=" O VAL B 210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.985A pdb=" N ILE A 268 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 279 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 182 through 184 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA7, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.501A pdb=" N THR A 637 " --> pdb=" O GLU A 705 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.243A pdb=" N LEU B 82 " --> pdb=" O GLY B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100 removed outlier: 6.565A pdb=" N VAL B 99 " --> pdb=" O ARG C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155 Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.978A pdb=" N GLY C 142 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 189 removed outlier: 3.501A pdb=" N THR C 192 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 369 through 370 Processing sheet with id=AB7, first strand: chain 'C' and resid 381 through 383 Processing sheet with id=AB8, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.683A pdb=" N PHE D 81 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 36 through 38 removed outlier: 6.411A pdb=" N LYS D 37 " --> pdb=" O TYR D 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 115 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D 100 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 136 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 141 Processing sheet with id=AC3, first strand: chain 'D' and resid 145 through 148 Processing sheet with id=AC4, first strand: chain 'D' and resid 216 through 219 Processing sheet with id=AC5, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AC6, first strand: chain 'D' and resid 246 through 248 Processing sheet with id=AC7, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.716A pdb=" N ALA E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.399A pdb=" N LEU E 56 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR E 72 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP E 58 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AD1, first strand: chain 'F' and resid 33 through 34 removed outlier: 6.906A pdb=" N ILE F 57 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE F 73 " --> pdb=" O ILE F 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP F 59 " --> pdb=" O MET F 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.754A pdb=" N ASP F 135 " --> pdb=" O ARG F 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 27 through 30 removed outlier: 3.841A pdb=" N ASP G 98 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 33 through 35 removed outlier: 5.885A pdb=" N LEU G 34 " --> pdb=" O GLU G 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 81 through 82 removed outlier: 6.453A pdb=" N TRP G 63 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR G 77 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 61 " --> pdb=" O TYR G 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 26 through 30 Processing sheet with id=AD7, first strand: chain 'H' and resid 34 through 35 removed outlier: 4.011A pdb=" N SER H 56 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL H 57 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER H 73 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP H 59 " --> pdb=" O VAL H 71 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1647 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: 3.17 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4967 1.35 - 1.47: 3997 1.47 - 1.59: 6937 1.59 - 1.71: 0 1.71 - 1.83: 111 Bond restraints: 16012 Sorted by residual: bond pdb=" N THR B 38 " pdb=" CA THR B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ASP E 24 " pdb=" CA ASP E 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLU H 24 " pdb=" CA GLU H 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASN C 81 " pdb=" CA ASN C 81 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP G 24 " pdb=" CA ASP G 24 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 ... (remaining 16007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 21149 1.40 - 2.79: 502 2.79 - 4.19: 110 4.19 - 5.59: 15 5.59 - 6.99: 7 Bond angle restraints: 21783 Sorted by residual: angle pdb=" C3 MAN K 4 " pdb=" C2 MAN K 4 " pdb=" O2 MAN K 4 " ideal model delta sigma weight residual 111.77 104.78 6.99 3.00e+00 1.11e-01 5.42e+00 angle pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" O2 BMA K 3 " ideal model delta sigma weight residual 112.95 106.23 6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 107.73 110.68 -2.95 1.34e+00 5.57e-01 4.85e+00 angle pdb=" CA CYS D 150 " pdb=" C CYS D 150 " pdb=" N ARG D 151 " ideal model delta sigma weight residual 114.76 117.26 -2.50 1.14e+00 7.69e-01 4.80e+00 angle pdb=" C3 MAN K 6 " pdb=" C2 MAN K 6 " pdb=" O2 MAN K 6 " ideal model delta sigma weight residual 111.77 105.22 6.55 3.00e+00 1.11e-01 4.77e+00 ... (remaining 21778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8662 17.79 - 35.59: 579 35.59 - 53.38: 104 53.38 - 71.18: 28 71.18 - 88.97: 16 Dihedral angle restraints: 9389 sinusoidal: 3733 harmonic: 5656 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS C 343 " pdb=" CB CYS C 343 " ideal model delta sinusoidal sigma weight residual -86.00 -155.94 69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS A 571 " pdb=" SG CYS A 571 " pdb=" SG CYS A 624 " pdb=" CB CYS A 624 " ideal model delta sinusoidal sigma weight residual -86.00 -148.26 62.26 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 9386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2197 0.057 - 0.114: 301 0.114 - 0.170: 57 0.170 - 0.227: 1 0.227 - 0.284: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 85 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 365 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 2554 not shown) Planarity restraints: 2749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 364 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 123 " 0.017 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE F 123 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE F 123 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 123 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 123 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 123 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 123 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 102 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" CD GLN E 102 " 0.026 2.00e-02 2.50e+03 pdb=" OE1 GLN E 102 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN E 102 " -0.009 2.00e-02 2.50e+03 ... (remaining 2746 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 253 2.66 - 3.22: 14970 3.22 - 3.78: 23470 3.78 - 4.34: 34581 4.34 - 4.90: 56461 Nonbonded interactions: 129735 Sorted by model distance: nonbonded pdb=" NE2 GLN F 62 " pdb=" O GLN F 66 " model vdw 2.098 3.120 nonbonded pdb=" NH1 ARG A 264 " pdb=" OE1 GLU A 276 " model vdw 2.144 3.120 nonbonded pdb=" O LEU A 626 " pdb=" OG1 THR A 627 " model vdw 2.217 3.040 nonbonded pdb=" O GLN G 29 " pdb=" NE2 GLN G 128 " model vdw 2.226 3.120 nonbonded pdb=" O PRO C 345 " pdb=" NH2 ARG C 349 " model vdw 2.229 3.120 ... (remaining 129730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16050 Z= 0.154 Angle : 0.567 6.986 21881 Z= 0.280 Chirality : 0.043 0.284 2557 Planarity : 0.003 0.047 2735 Dihedral : 12.923 88.969 5691 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1887 helix: 1.29 (0.27), residues: 397 sheet: 0.62 (0.23), residues: 483 loop : 0.09 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 124 TYR 0.016 0.001 TYR H 136 PHE 0.027 0.001 PHE F 123 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (16012) covalent geometry : angle 0.55671 / 0.28 (21783) SS BOND : bond 0.00277 / 0.12 ( 16) SS BOND : angle 1.16070 / 0.61 ( 32) hydrogen bonds : bond 0.17915 / 11.63 ( 622) hydrogen bonds : angle 7.16525 / 5.04 ( 1647) link_ALPHA1-2 : bond 0.00629 / 0.33 ( 1) link_ALPHA1-2 : angle 2.59617 / 1.24 ( 3) link_ALPHA1-3 : bond 0.00594 / 0.30 ( 2) link_ALPHA1-3 : angle 2.54971 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00808 / 0.43 ( 1) link_ALPHA1-6 : angle 1.36467 / 0.72 ( 3) link_BETA1-4 : bond 0.00496 / 0.25 ( 4) link_BETA1-4 : angle 2.62463 / 1.14 ( 12) link_NAG-ASN : bond 0.00200 / 0.13 ( 14) link_NAG-ASN : angle 1.54641 / 0.85 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 LYS cc_start: 0.9269 (tmmt) cc_final: 0.8529 (tmmt) REVERT: C 147 MET cc_start: 0.8743 (mmm) cc_final: 0.8530 (mmm) REVERT: C 377 MET cc_start: 0.8237 (mmp) cc_final: 0.7793 (mmp) REVERT: C 462 TRP cc_start: 0.8412 (p90) cc_final: 0.8140 (p90) REVERT: D 31 LEU cc_start: 0.9196 (tt) cc_final: 0.8989 (tp) REVERT: D 33 ASN cc_start: 0.7998 (t0) cc_final: 0.7613 (t0) REVERT: D 58 GLN cc_start: 0.8174 (tp40) cc_final: 0.7959 (tp40) REVERT: D 176 GLN cc_start: 0.8415 (mt0) cc_final: 0.8206 (mt0) REVERT: G 70 GLN cc_start: 0.8363 (mt0) cc_final: 0.8108 (mt0) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 0.6675 time to fit residues: 219.6458 Evaluate side-chains 235 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 134 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN D 106 GLN D 116 HIS D 162 HIS F 24 GLN F 62 GLN F 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095264 restraints weight = 26968.784| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.65 r_work: 0.3144 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16050 Z= 0.155 Angle : 0.607 7.588 21881 Z= 0.313 Chirality : 0.044 0.184 2557 Planarity : 0.004 0.041 2735 Dihedral : 4.583 28.239 2110 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 9.47 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1887 helix: 1.40 (0.27), residues: 406 sheet: 0.72 (0.24), residues: 476 loop : -0.00 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 41 TYR 0.021 0.002 TYR D 206 PHE 0.023 0.002 PHE H 52 TRP 0.010 0.001 TRP C 183 HIS 0.009 0.001 HIS D 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (16012) covalent geometry : angle 0.60076 / 0.31 (21783) SS BOND : bond 0.00386 / 0.22 ( 16) SS BOND : angle 1.08767 / 0.64 ( 32) hydrogen bonds : bond 0.04070 / 2.66 ( 622) hydrogen bonds : angle 5.51869 / 3.92 ( 1647) link_ALPHA1-2 : bond 0.00065 / 0.03 ( 1) link_ALPHA1-2 : angle 1.87874 / 0.77 ( 3) link_ALPHA1-3 : bond 0.00441 / 0.22 ( 2) link_ALPHA1-3 : angle 1.48855 / 0.65 ( 6) link_ALPHA1-6 : bond 0.00922 / 0.49 ( 1) link_ALPHA1-6 : angle 1.37352 / 0.75 ( 3) link_BETA1-4 : bond 0.00225 / 0.11 ( 4) link_BETA1-4 : angle 1.89905 / 0.83 ( 12) link_NAG-ASN : bond 0.00201 / 0.12 ( 14) link_NAG-ASN : angle 1.49064 / 0.86 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7958 (pm20) cc_final: 0.7716 (pm20) REVERT: A 285 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8785 (tt0) REVERT: A 534 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7613 (mtm180) REVERT: B 64 LYS cc_start: 0.9418 (tmmt) cc_final: 0.9211 (tmmm) REVERT: C 377 MET cc_start: 0.8573 (mmp) cc_final: 0.8235 (mmp) REVERT: C 435 GLN cc_start: 0.7921 (pp30) cc_final: 0.7713 (pp30) REVERT: D 33 ASN cc_start: 0.8514 (t0) cc_final: 0.8112 (t0) REVERT: D 43 SER cc_start: 0.8301 (t) cc_final: 0.8098 (t) REVERT: D 48 ARG cc_start: 0.7495 (ptm-80) cc_final: 0.7183 (ptp90) REVERT: D 58 GLN cc_start: 0.8372 (tp40) cc_final: 0.7922 (tp40) REVERT: D 74 GLU cc_start: 0.6964 (tt0) cc_final: 0.6347 (tp30) REVERT: D 173 ASP cc_start: 0.8696 (t0) cc_final: 0.8326 (t70) REVERT: D 176 GLN cc_start: 0.8572 (mt0) cc_final: 0.8133 (mt0) REVERT: D 215 ASP cc_start: 0.7792 (p0) cc_final: 0.7512 (p0) REVERT: E 68 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7849 (ttpt) REVERT: F 50 TYR cc_start: 0.8618 (p90) cc_final: 0.7724 (p90) REVERT: F 104 MET cc_start: 0.8308 (tmm) cc_final: 0.7902 (tmm) REVERT: F 112 GLU cc_start: 0.8778 (pt0) cc_final: 0.8058 (pm20) REVERT: F 124 ARG cc_start: 0.8349 (mtt-85) cc_final: 0.7883 (mpt90) REVERT: G 70 GLN cc_start: 0.8403 (mt0) cc_final: 0.8156 (mt0) REVERT: G 121 GLN cc_start: 0.8185 (mt0) cc_final: 0.7890 (mp10) REVERT: H 25 GLU cc_start: 0.8397 (mp0) cc_final: 0.7999 (mp0) REVERT: H 96 ASP cc_start: 0.8488 (t70) cc_final: 0.8174 (t70) REVERT: H 112 GLU cc_start: 0.7815 (pm20) cc_final: 0.7559 (pm20) outliers start: 30 outliers final: 12 residues processed: 264 average time/residue: 0.6687 time to fit residues: 193.8107 Evaluate side-chains 238 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 chunk 170 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 HIS B 115 ASN D 116 HIS D 162 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095991 restraints weight = 27249.630| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.72 r_work: 0.3132 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16050 Z= 0.136 Angle : 0.567 8.738 21881 Z= 0.289 Chirality : 0.043 0.184 2557 Planarity : 0.004 0.046 2735 Dihedral : 4.452 19.721 2108 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.46 % Allowed : 12.22 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1887 helix: 1.41 (0.27), residues: 407 sheet: 0.62 (0.23), residues: 479 loop : -0.07 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 41 TYR 0.018 0.001 TYR D 206 PHE 0.015 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16012) covalent geometry : angle 0.56112 / 0.29 (21783) SS BOND : bond 0.00290 / 0.18 ( 16) SS BOND : angle 0.78174 / 0.47 ( 32) hydrogen bonds : bond 0.03630 / 2.36 ( 622) hydrogen bonds : angle 5.14453 / 3.66 ( 1647) link_ALPHA1-2 : bond 0.00003 / 0.00 ( 1) link_ALPHA1-2 : angle 1.64650 / 0.75 ( 3) link_ALPHA1-3 : bond 0.00477 / 0.24 ( 2) link_ALPHA1-3 : angle 1.59300 / 0.70 ( 6) link_ALPHA1-6 : bond 0.00882 / 0.46 ( 1) link_ALPHA1-6 : angle 1.24241 / 0.66 ( 3) link_BETA1-4 : bond 0.00229 / 0.11 ( 4) link_BETA1-4 : angle 1.78365 / 0.78 ( 12) link_NAG-ASN : bond 0.00155 / 0.10 ( 14) link_NAG-ASN : angle 1.48127 / 0.86 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8248 (pm20) cc_final: 0.7998 (pm20) REVERT: A 193 GLN cc_start: 0.7800 (pm20) cc_final: 0.7596 (pm20) REVERT: A 285 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: A 529 ASP cc_start: 0.8194 (p0) cc_final: 0.7748 (p0) REVERT: B 54 CYS cc_start: 0.8716 (p) cc_final: 0.8342 (p) REVERT: B 112 LEU cc_start: 0.8811 (pp) cc_final: 0.8417 (pt) REVERT: C 215 GLN cc_start: 0.8660 (mt0) cc_final: 0.8140 (mm110) REVERT: C 370 THR cc_start: 0.9258 (m) cc_final: 0.9005 (m) REVERT: C 377 MET cc_start: 0.8346 (mmp) cc_final: 0.8129 (mmp) REVERT: C 435 GLN cc_start: 0.7961 (pp30) cc_final: 0.7655 (pp30) REVERT: D 29 SER cc_start: 0.7804 (t) cc_final: 0.7554 (p) REVERT: D 31 LEU cc_start: 0.9259 (tt) cc_final: 0.9038 (tp) REVERT: D 33 ASN cc_start: 0.8504 (t0) cc_final: 0.8094 (t0) REVERT: D 43 SER cc_start: 0.8137 (t) cc_final: 0.7872 (t) REVERT: D 48 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7093 (ptp90) REVERT: D 58 GLN cc_start: 0.8262 (tp40) cc_final: 0.7724 (tp40) REVERT: D 74 GLU cc_start: 0.6654 (tt0) cc_final: 0.6032 (tp30) REVERT: D 165 GLU cc_start: 0.7909 (mp0) cc_final: 0.6794 (mp0) REVERT: D 173 ASP cc_start: 0.8555 (t0) cc_final: 0.8162 (t70) REVERT: D 176 GLN cc_start: 0.8532 (mt0) cc_final: 0.8221 (mt0) REVERT: D 215 ASP cc_start: 0.7692 (p0) cc_final: 0.7372 (p0) REVERT: D 246 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7379 (mm110) REVERT: E 68 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7826 (ttpt) REVERT: E 126 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7784 (mttp) REVERT: F 50 TYR cc_start: 0.8536 (p90) cc_final: 0.7511 (p90) REVERT: F 104 MET cc_start: 0.8176 (tmm) cc_final: 0.7891 (tmm) REVERT: F 112 GLU cc_start: 0.8596 (pt0) cc_final: 0.7994 (pm20) REVERT: G 70 GLN cc_start: 0.8357 (mt0) cc_final: 0.8068 (mt0) REVERT: G 107 GLU cc_start: 0.6298 (OUTLIER) cc_final: 0.5669 (mm-30) REVERT: G 121 GLN cc_start: 0.8035 (mt0) cc_final: 0.7795 (mt0) REVERT: G 128 GLN cc_start: 0.8168 (pm20) cc_final: 0.7946 (pm20) REVERT: H 25 GLU cc_start: 0.8358 (mp0) cc_final: 0.7989 (mp0) REVERT: H 43 LEU cc_start: 0.8407 (mt) cc_final: 0.8192 (mp) REVERT: H 96 ASP cc_start: 0.8543 (t70) cc_final: 0.7534 (t70) REVERT: H 99 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7148 (mp0) REVERT: H 112 GLU cc_start: 0.7715 (pm20) cc_final: 0.7454 (pm20) REVERT: H 151 VAL cc_start: 0.8496 (t) cc_final: 0.8174 (m) outliers start: 42 outliers final: 21 residues processed: 269 average time/residue: 0.6288 time to fit residues: 186.8803 Evaluate side-chains 255 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 231 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 3 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 370 GLN ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 106 GLN D 116 HIS F 24 GLN F 66 GLN H 97 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093978 restraints weight = 27151.724| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.67 r_work: 0.3118 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16050 Z= 0.177 Angle : 0.581 7.521 21881 Z= 0.296 Chirality : 0.043 0.180 2557 Planarity : 0.004 0.041 2735 Dihedral : 4.527 19.040 2108 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.98 % Allowed : 13.39 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1887 helix: 1.41 (0.26), residues: 407 sheet: 0.51 (0.23), residues: 483 loop : -0.10 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 41 TYR 0.021 0.002 TYR D 206 PHE 0.017 0.002 PHE A 304 TRP 0.011 0.002 TRP H 70 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16012) covalent geometry : angle 0.57414 / 0.29 (21783) SS BOND : bond 0.00376 / 0.24 ( 16) SS BOND : angle 0.83968 / 0.49 ( 32) hydrogen bonds : bond 0.03658 / 2.40 ( 622) hydrogen bonds : angle 5.02174 / 3.57 ( 1647) link_ALPHA1-2 : bond 0.00178 / 0.09 ( 1) link_ALPHA1-2 : angle 1.77491 / 0.80 ( 3) link_ALPHA1-3 : bond 0.00365 / 0.18 ( 2) link_ALPHA1-3 : angle 1.62532 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00619 / 0.33 ( 1) link_ALPHA1-6 : angle 1.09020 / 0.55 ( 3) link_BETA1-4 : bond 0.00169 / 0.08 ( 4) link_BETA1-4 : angle 1.83596 / 0.81 ( 12) link_NAG-ASN : bond 0.00213 / 0.14 ( 14) link_NAG-ASN : angle 1.55658 / 0.91 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7616 (mmm-85) REVERT: A 193 GLN cc_start: 0.8090 (pm20) cc_final: 0.7845 (pm20) REVERT: A 548 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8412 (t) REVERT: A 619 ASP cc_start: 0.8149 (t0) cc_final: 0.7937 (t0) REVERT: B 54 CYS cc_start: 0.8932 (p) cc_final: 0.8582 (p) REVERT: B 64 LYS cc_start: 0.9339 (tmmm) cc_final: 0.9041 (tmmm) REVERT: B 112 LEU cc_start: 0.8949 (pp) cc_final: 0.8507 (pt) REVERT: C 215 GLN cc_start: 0.8685 (mt0) cc_final: 0.8248 (mt0) REVERT: C 370 THR cc_start: 0.9282 (m) cc_final: 0.8999 (m) REVERT: C 435 GLN cc_start: 0.8029 (pp30) cc_final: 0.7653 (pp30) REVERT: D 29 SER cc_start: 0.7953 (t) cc_final: 0.7720 (p) REVERT: D 31 LEU cc_start: 0.9239 (tt) cc_final: 0.9029 (tp) REVERT: D 33 ASN cc_start: 0.8558 (t0) cc_final: 0.8141 (t0) REVERT: D 43 SER cc_start: 0.8255 (t) cc_final: 0.8011 (t) REVERT: D 48 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: D 58 GLN cc_start: 0.8411 (tp40) cc_final: 0.7856 (tp40) REVERT: D 74 GLU cc_start: 0.7014 (tt0) cc_final: 0.6351 (tp30) REVERT: D 173 ASP cc_start: 0.8672 (t0) cc_final: 0.8249 (t70) REVERT: D 176 GLN cc_start: 0.8650 (mt0) cc_final: 0.8361 (mt0) REVERT: D 215 ASP cc_start: 0.7802 (p0) cc_final: 0.7467 (p0) REVERT: E 68 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7978 (ttpt) REVERT: F 42 LYS cc_start: 0.8758 (tttt) cc_final: 0.8524 (tptm) REVERT: F 88 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8323 (mt0) REVERT: F 104 MET cc_start: 0.8252 (tmm) cc_final: 0.7893 (tmm) REVERT: F 112 GLU cc_start: 0.8772 (pt0) cc_final: 0.8162 (pm20) REVERT: G 70 GLN cc_start: 0.8134 (mt0) cc_final: 0.7853 (mt0) REVERT: G 107 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5759 (mm-30) REVERT: G 121 GLN cc_start: 0.8045 (mt0) cc_final: 0.7826 (mt0) REVERT: H 25 GLU cc_start: 0.8422 (mp0) cc_final: 0.8066 (mp0) REVERT: H 42 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7174 (tmm-80) REVERT: H 66 LYS cc_start: 0.7283 (mppt) cc_final: 0.6851 (mppt) REVERT: H 96 ASP cc_start: 0.8326 (t70) cc_final: 0.7444 (t70) REVERT: H 99 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7217 (mp0) REVERT: H 112 GLU cc_start: 0.7826 (pm20) cc_final: 0.7525 (pm20) REVERT: H 151 VAL cc_start: 0.8527 (t) cc_final: 0.8136 (m) outliers start: 51 outliers final: 25 residues processed: 267 average time/residue: 0.5889 time to fit residues: 173.7251 Evaluate side-chains 259 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 119 GLN Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 ARG Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 42 ARG Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 174 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS D 116 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096284 restraints weight = 27213.706| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.71 r_work: 0.3143 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16050 Z= 0.114 Angle : 0.542 7.290 21881 Z= 0.276 Chirality : 0.042 0.181 2557 Planarity : 0.004 0.040 2735 Dihedral : 4.350 17.363 2108 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.81 % Allowed : 14.85 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1887 helix: 1.48 (0.26), residues: 407 sheet: 0.54 (0.23), residues: 491 loop : -0.06 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 41 TYR 0.018 0.001 TYR D 206 PHE 0.017 0.001 PHE A 304 TRP 0.011 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (16012) covalent geometry : angle 0.53680 / 0.28 (21783) SS BOND : bond 0.00327 / 0.22 ( 16) SS BOND : angle 0.69565 / 0.42 ( 32) hydrogen bonds : bond 0.03158 / 2.06 ( 622) hydrogen bonds : angle 4.86396 / 3.46 ( 1647) link_ALPHA1-2 : bond 0.00066 / 0.03 ( 1) link_ALPHA1-2 : angle 1.57538 / 0.70 ( 3) link_ALPHA1-3 : bond 0.00464 / 0.23 ( 2) link_ALPHA1-3 : angle 1.55519 / 0.67 ( 6) link_ALPHA1-6 : bond 0.00941 / 0.50 ( 1) link_ALPHA1-6 : angle 1.17648 / 0.60 ( 3) link_BETA1-4 : bond 0.00215 / 0.11 ( 4) link_BETA1-4 : angle 1.69904 / 0.74 ( 12) link_NAG-ASN : bond 0.00139 / 0.08 ( 14) link_NAG-ASN : angle 1.40615 / 0.82 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 249 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7688 (mmm-85) REVERT: A 117 ARG cc_start: 0.8361 (tpm-80) cc_final: 0.8129 (tpm-80) REVERT: A 193 GLN cc_start: 0.7944 (pm20) cc_final: 0.7708 (pm20) REVERT: A 285 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: A 596 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 619 ASP cc_start: 0.8108 (t0) cc_final: 0.7844 (t0) REVERT: B 54 CYS cc_start: 0.8731 (p) cc_final: 0.8414 (p) REVERT: B 64 LYS cc_start: 0.9388 (tmmm) cc_final: 0.9013 (tmmm) REVERT: C 147 MET cc_start: 0.8952 (mmm) cc_final: 0.8690 (mmm) REVERT: C 197 ASP cc_start: 0.8834 (p0) cc_final: 0.8407 (p0) REVERT: C 215 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: C 370 THR cc_start: 0.9292 (m) cc_final: 0.9031 (m) REVERT: C 377 MET cc_start: 0.8656 (mmp) cc_final: 0.8181 (mmt) REVERT: D 29 SER cc_start: 0.7884 (t) cc_final: 0.7678 (p) REVERT: D 31 LEU cc_start: 0.9204 (tt) cc_final: 0.8984 (tp) REVERT: D 33 ASN cc_start: 0.8499 (t0) cc_final: 0.8077 (t0) REVERT: D 40 GLN cc_start: 0.7593 (pp30) cc_final: 0.7174 (tm130) REVERT: D 43 SER cc_start: 0.8046 (t) cc_final: 0.7767 (t) REVERT: D 48 ARG cc_start: 0.7340 (ptm-80) cc_final: 0.7041 (ptp90) REVERT: D 58 GLN cc_start: 0.8275 (tp40) cc_final: 0.7676 (tp40) REVERT: D 74 GLU cc_start: 0.6672 (tt0) cc_final: 0.6175 (tp30) REVERT: D 173 ASP cc_start: 0.8508 (t0) cc_final: 0.8076 (t70) REVERT: D 176 GLN cc_start: 0.8560 (mt0) cc_final: 0.8236 (mt0) REVERT: D 196 LYS cc_start: 0.6421 (OUTLIER) cc_final: 0.6035 (mtmm) REVERT: D 215 ASP cc_start: 0.7662 (p0) cc_final: 0.7362 (p0) REVERT: E 68 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7912 (ttpt) REVERT: F 42 LYS cc_start: 0.8730 (tttt) cc_final: 0.8507 (tptm) REVERT: F 88 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8284 (mt0) REVERT: F 93 MET cc_start: 0.8726 (mtt) cc_final: 0.8483 (mtt) REVERT: F 104 MET cc_start: 0.8162 (tmm) cc_final: 0.7840 (tmm) REVERT: F 112 GLU cc_start: 0.8574 (pt0) cc_final: 0.8002 (pm20) REVERT: G 27 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7454 (mmm) REVERT: G 70 GLN cc_start: 0.8096 (mt0) cc_final: 0.7775 (mt0) REVERT: G 107 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5729 (mm-30) REVERT: G 121 GLN cc_start: 0.7986 (mt0) cc_final: 0.7677 (mp10) REVERT: H 25 GLU cc_start: 0.8351 (mp0) cc_final: 0.8031 (mp0) REVERT: H 66 LYS cc_start: 0.7383 (mppt) cc_final: 0.6912 (mppt) REVERT: H 96 ASP cc_start: 0.8334 (t70) cc_final: 0.7411 (t70) REVERT: H 99 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7131 (mp0) REVERT: H 107 ASN cc_start: 0.8211 (m-40) cc_final: 0.7944 (m-40) REVERT: H 112 GLU cc_start: 0.7753 (pm20) cc_final: 0.7477 (pm20) REVERT: H 151 VAL cc_start: 0.8438 (t) cc_final: 0.8096 (m) outliers start: 48 outliers final: 19 residues processed: 273 average time/residue: 0.5969 time to fit residues: 180.1970 Evaluate side-chains 259 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 285 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 107 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 155 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 120 optimal weight: 0.0570 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096643 restraints weight = 27052.564| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.72 r_work: 0.3147 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16050 Z= 0.103 Angle : 0.535 7.763 21881 Z= 0.272 Chirality : 0.041 0.180 2557 Planarity : 0.004 0.038 2735 Dihedral : 4.279 28.165 2108 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.34 % Allowed : 16.43 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1887 helix: 1.48 (0.26), residues: 407 sheet: 0.60 (0.23), residues: 491 loop : -0.04 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 41 TYR 0.019 0.001 TYR A 682 PHE 0.018 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (16012) covalent geometry : angle 0.52864 / 0.27 (21783) SS BOND : bond 0.00310 / 0.19 ( 16) SS BOND : angle 1.16801 / 0.62 ( 32) hydrogen bonds : bond 0.03025 / 1.97 ( 622) hydrogen bonds : angle 4.75203 / 3.37 ( 1647) link_ALPHA1-2 : bond 0.00099 / 0.05 ( 1) link_ALPHA1-2 : angle 1.56611 / 0.71 ( 3) link_ALPHA1-3 : bond 0.00428 / 0.21 ( 2) link_ALPHA1-3 : angle 1.56832 / 0.66 ( 6) link_ALPHA1-6 : bond 0.00890 / 0.47 ( 1) link_ALPHA1-6 : angle 1.22063 / 0.62 ( 3) link_BETA1-4 : bond 0.00245 / 0.12 ( 4) link_BETA1-4 : angle 1.66958 / 0.72 ( 12) link_NAG-ASN : bond 0.00141 / 0.09 ( 14) link_NAG-ASN : angle 1.37418 / 0.80 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.7940 (pm20) cc_final: 0.7702 (pm20) REVERT: A 596 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 619 ASP cc_start: 0.8091 (t0) cc_final: 0.7844 (t0) REVERT: A 622 THR cc_start: 0.8857 (p) cc_final: 0.8511 (t) REVERT: B 54 CYS cc_start: 0.8666 (p) cc_final: 0.8383 (p) REVERT: B 64 LYS cc_start: 0.9401 (tmmm) cc_final: 0.9086 (tmmm) REVERT: C 197 ASP cc_start: 0.8821 (p0) cc_final: 0.8402 (p0) REVERT: C 215 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: C 370 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9081 (p) REVERT: C 377 MET cc_start: 0.8588 (mmp) cc_final: 0.7925 (mpt) REVERT: D 33 ASN cc_start: 0.8496 (t0) cc_final: 0.8066 (t0) REVERT: D 40 GLN cc_start: 0.7585 (pp30) cc_final: 0.7109 (tm130) REVERT: D 43 SER cc_start: 0.8025 (t) cc_final: 0.7699 (t) REVERT: D 58 GLN cc_start: 0.8244 (tp40) cc_final: 0.7607 (tp40) REVERT: D 61 MET cc_start: 0.7056 (mmm) cc_final: 0.6711 (mmp) REVERT: D 74 GLU cc_start: 0.6629 (tt0) cc_final: 0.6260 (tp30) REVERT: D 173 ASP cc_start: 0.8374 (t0) cc_final: 0.7905 (t70) REVERT: D 175 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8032 (mtp-110) REVERT: D 176 GLN cc_start: 0.8562 (mt0) cc_final: 0.8137 (mt0) REVERT: D 196 LYS cc_start: 0.6437 (OUTLIER) cc_final: 0.6005 (mtmm) REVERT: D 215 ASP cc_start: 0.7655 (p0) cc_final: 0.7348 (p0) REVERT: E 68 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7926 (ttpt) REVERT: F 42 LYS cc_start: 0.8705 (tttt) cc_final: 0.8485 (tptm) REVERT: F 88 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8285 (mt0) REVERT: F 93 MET cc_start: 0.8723 (mtt) cc_final: 0.8402 (mtt) REVERT: F 104 MET cc_start: 0.8141 (tmm) cc_final: 0.7831 (tmm) REVERT: F 112 GLU cc_start: 0.8528 (pt0) cc_final: 0.7981 (pm20) REVERT: G 70 GLN cc_start: 0.8351 (mt0) cc_final: 0.8037 (mt0) REVERT: G 107 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5771 (mm-30) REVERT: H 25 GLU cc_start: 0.8342 (mp0) cc_final: 0.8015 (mp0) REVERT: H 66 LYS cc_start: 0.7402 (mppt) cc_final: 0.7124 (mppt) REVERT: H 96 ASP cc_start: 0.8320 (t70) cc_final: 0.7386 (t70) REVERT: H 99 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7112 (mp0) REVERT: H 112 GLU cc_start: 0.7736 (pm20) cc_final: 0.7404 (pm20) REVERT: H 151 VAL cc_start: 0.8420 (t) cc_final: 0.8085 (m) outliers start: 40 outliers final: 18 residues processed: 269 average time/residue: 0.5822 time to fit residues: 174.2010 Evaluate side-chains 245 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 80 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 177 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN D 116 HIS F 24 GLN F 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.096192 restraints weight = 27176.119| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.74 r_work: 0.3138 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16050 Z= 0.123 Angle : 0.543 8.710 21881 Z= 0.275 Chirality : 0.042 0.178 2557 Planarity : 0.004 0.037 2735 Dihedral : 4.252 24.276 2108 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.40 % Allowed : 17.37 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 1887 helix: 1.50 (0.26), residues: 407 sheet: 0.62 (0.23), residues: 492 loop : -0.04 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 41 TYR 0.014 0.001 TYR D 206 PHE 0.020 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16012) covalent geometry : angle 0.53683 / 0.27 (21783) SS BOND : bond 0.00278 / 0.18 ( 16) SS BOND : angle 0.93173 / 0.48 ( 32) hydrogen bonds : bond 0.03118 / 2.03 ( 622) hydrogen bonds : angle 4.69965 / 3.33 ( 1647) link_ALPHA1-2 : bond 0.00056 / 0.03 ( 1) link_ALPHA1-2 : angle 1.61419 / 0.73 ( 3) link_ALPHA1-3 : bond 0.00349 / 0.17 ( 2) link_ALPHA1-3 : angle 1.60486 / 0.69 ( 6) link_ALPHA1-6 : bond 0.00765 / 0.40 ( 1) link_ALPHA1-6 : angle 1.21240 / 0.61 ( 3) link_BETA1-4 : bond 0.00183 / 0.09 ( 4) link_BETA1-4 : angle 1.71185 / 0.75 ( 12) link_NAG-ASN : bond 0.00144 / 0.09 ( 14) link_NAG-ASN : angle 1.42996 / 0.83 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: A 88 TYR cc_start: 0.8794 (m-80) cc_final: 0.8498 (m-80) REVERT: A 117 ARG cc_start: 0.8361 (tpm-80) cc_final: 0.8146 (tpm-80) REVERT: A 122 LEU cc_start: 0.8028 (mt) cc_final: 0.7768 (mm) REVERT: A 193 GLN cc_start: 0.7880 (pm20) cc_final: 0.7675 (pm20) REVERT: A 380 MET cc_start: 0.8303 (mmm) cc_final: 0.8073 (mmm) REVERT: A 596 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 619 ASP cc_start: 0.8118 (t0) cc_final: 0.7872 (t0) REVERT: A 622 THR cc_start: 0.8875 (p) cc_final: 0.8516 (t) REVERT: B 54 CYS cc_start: 0.8645 (p) cc_final: 0.8367 (p) REVERT: B 64 LYS cc_start: 0.9410 (tmmm) cc_final: 0.9114 (tmmm) REVERT: C 197 ASP cc_start: 0.8819 (p0) cc_final: 0.8406 (p0) REVERT: C 215 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: C 366 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7776 (mm-30) REVERT: C 370 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9040 (p) REVERT: C 377 MET cc_start: 0.8627 (mmp) cc_final: 0.8239 (mpt) REVERT: D 33 ASN cc_start: 0.8434 (t0) cc_final: 0.8055 (t0) REVERT: D 43 SER cc_start: 0.8050 (t) cc_final: 0.7807 (t) REVERT: D 58 GLN cc_start: 0.8255 (tp40) cc_final: 0.7607 (tp40) REVERT: D 61 MET cc_start: 0.7121 (mmm) cc_final: 0.6806 (mmp) REVERT: D 74 GLU cc_start: 0.6428 (tt0) cc_final: 0.6190 (tp30) REVERT: D 173 ASP cc_start: 0.8393 (t0) cc_final: 0.7910 (t70) REVERT: D 176 GLN cc_start: 0.8566 (mt0) cc_final: 0.8139 (mt0) REVERT: D 215 ASP cc_start: 0.7655 (p0) cc_final: 0.7337 (p0) REVERT: D 306 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7602 (m) REVERT: E 68 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7906 (ttpt) REVERT: F 42 LYS cc_start: 0.8724 (tttt) cc_final: 0.8491 (tptm) REVERT: F 88 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8310 (mt0) REVERT: F 93 MET cc_start: 0.8743 (mtt) cc_final: 0.8429 (mtt) REVERT: F 104 MET cc_start: 0.8135 (tmm) cc_final: 0.7814 (tmm) REVERT: F 112 GLU cc_start: 0.8526 (pt0) cc_final: 0.7984 (pm20) REVERT: G 70 GLN cc_start: 0.8350 (mt0) cc_final: 0.8052 (mt0) REVERT: G 76 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7827 (mp) REVERT: G 89 ARG cc_start: 0.8069 (ptt90) cc_final: 0.7557 (ptm-80) REVERT: G 107 GLU cc_start: 0.6157 (mm-30) cc_final: 0.5633 (mm-30) REVERT: G 121 GLN cc_start: 0.8145 (mt0) cc_final: 0.7923 (mp10) REVERT: H 66 LYS cc_start: 0.7388 (mppt) cc_final: 0.7108 (mppt) REVERT: H 96 ASP cc_start: 0.8419 (t70) cc_final: 0.7548 (t70) REVERT: H 99 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7134 (mp0) REVERT: H 112 GLU cc_start: 0.7700 (pm20) cc_final: 0.7421 (pm20) REVERT: H 151 VAL cc_start: 0.8454 (t) cc_final: 0.8104 (m) outliers start: 41 outliers final: 26 residues processed: 256 average time/residue: 0.5926 time to fit residues: 168.4395 Evaluate side-chains 257 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 12 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 0.0970 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 66 GLN H 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096004 restraints weight = 27383.623| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.70 r_work: 0.3136 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16050 Z= 0.132 Angle : 0.553 9.700 21881 Z= 0.280 Chirality : 0.042 0.177 2557 Planarity : 0.004 0.037 2735 Dihedral : 4.283 24.054 2108 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.75 % Allowed : 17.54 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 1887 helix: 1.51 (0.26), residues: 407 sheet: 0.66 (0.23), residues: 484 loop : -0.03 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 41 TYR 0.022 0.001 TYR A 682 PHE 0.023 0.001 PHE A 304 TRP 0.009 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16012) covalent geometry : angle 0.54729 / 0.28 (21783) SS BOND : bond 0.00351 / 0.21 ( 16) SS BOND : angle 0.88999 / 0.46 ( 32) hydrogen bonds : bond 0.03167 / 2.06 ( 622) hydrogen bonds : angle 4.69311 / 3.32 ( 1647) link_ALPHA1-2 : bond 0.00014 / 0.01 ( 1) link_ALPHA1-2 : angle 1.63935 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00326 / 0.16 ( 2) link_ALPHA1-3 : angle 1.60400 / 0.69 ( 6) link_ALPHA1-6 : bond 0.00732 / 0.39 ( 1) link_ALPHA1-6 : angle 1.18220 / 0.58 ( 3) link_BETA1-4 : bond 0.00158 / 0.08 ( 4) link_BETA1-4 : angle 1.74226 / 0.76 ( 12) link_NAG-ASN : bond 0.00154 / 0.09 ( 14) link_NAG-ASN : angle 1.43780 / 0.84 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8830 (m-80) cc_final: 0.8565 (m-80) REVERT: A 122 LEU cc_start: 0.8050 (mt) cc_final: 0.7783 (mm) REVERT: A 193 GLN cc_start: 0.7899 (pm20) cc_final: 0.7654 (pm20) REVERT: A 380 MET cc_start: 0.8376 (mmm) cc_final: 0.8167 (mmm) REVERT: A 596 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8575 (mm) REVERT: A 619 ASP cc_start: 0.8129 (t0) cc_final: 0.7884 (t0) REVERT: A 622 THR cc_start: 0.8887 (p) cc_final: 0.8526 (t) REVERT: B 54 CYS cc_start: 0.8653 (p) cc_final: 0.8367 (p) REVERT: B 64 LYS cc_start: 0.9413 (tmmm) cc_final: 0.9116 (tmmm) REVERT: B 237 GLN cc_start: 0.8718 (mp10) cc_final: 0.8373 (mp10) REVERT: C 197 ASP cc_start: 0.8812 (p0) cc_final: 0.8410 (p0) REVERT: C 215 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8214 (mm110) REVERT: C 366 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 370 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9040 (p) REVERT: C 377 MET cc_start: 0.8482 (mmp) cc_final: 0.8101 (mpt) REVERT: C 435 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: D 33 ASN cc_start: 0.8473 (t0) cc_final: 0.8085 (t0) REVERT: D 43 SER cc_start: 0.8056 (t) cc_final: 0.7812 (t) REVERT: D 58 GLN cc_start: 0.8272 (tp40) cc_final: 0.7628 (tp40) REVERT: D 61 MET cc_start: 0.7173 (mmm) cc_final: 0.6863 (mmp) REVERT: D 74 GLU cc_start: 0.6378 (tt0) cc_final: 0.6147 (tp30) REVERT: D 165 GLU cc_start: 0.7903 (mp0) cc_final: 0.7396 (mp0) REVERT: D 173 ASP cc_start: 0.8443 (t0) cc_final: 0.7968 (t70) REVERT: D 175 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8144 (mtp-110) REVERT: D 176 GLN cc_start: 0.8536 (mt0) cc_final: 0.8217 (mt0) REVERT: D 215 ASP cc_start: 0.7682 (p0) cc_final: 0.7359 (p0) REVERT: D 306 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7670 (m) REVERT: E 68 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7901 (ttpt) REVERT: F 42 LYS cc_start: 0.8732 (tttt) cc_final: 0.8440 (tptm) REVERT: F 93 MET cc_start: 0.8748 (mtt) cc_final: 0.8440 (mtt) REVERT: F 104 MET cc_start: 0.8144 (tmm) cc_final: 0.7789 (tmm) REVERT: F 112 GLU cc_start: 0.8534 (pt0) cc_final: 0.8001 (pm20) REVERT: G 70 GLN cc_start: 0.8149 (mt0) cc_final: 0.7837 (mt0) REVERT: G 76 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7841 (mp) REVERT: G 89 ARG cc_start: 0.8119 (ptt90) cc_final: 0.7736 (ptt-90) REVERT: G 107 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5666 (mm-30) REVERT: G 121 GLN cc_start: 0.8044 (mt0) cc_final: 0.7769 (mp10) REVERT: H 66 LYS cc_start: 0.7390 (mppt) cc_final: 0.7098 (mppt) REVERT: H 96 ASP cc_start: 0.8277 (t70) cc_final: 0.7355 (t70) REVERT: H 99 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7132 (mp0) REVERT: H 112 GLU cc_start: 0.7730 (pm20) cc_final: 0.7449 (pm20) REVERT: H 151 VAL cc_start: 0.8482 (t) cc_final: 0.8120 (m) outliers start: 47 outliers final: 27 residues processed: 259 average time/residue: 0.5848 time to fit residues: 168.2890 Evaluate side-chains 259 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN D 116 HIS F 24 GLN F 66 GLN G 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094218 restraints weight = 26992.892| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.66 r_work: 0.3124 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16050 Z= 0.173 Angle : 0.584 8.852 21881 Z= 0.296 Chirality : 0.043 0.175 2557 Planarity : 0.004 0.041 2735 Dihedral : 4.398 22.125 2108 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.46 % Allowed : 17.78 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.19), residues: 1887 helix: 1.47 (0.26), residues: 407 sheet: 0.61 (0.23), residues: 477 loop : -0.07 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 41 TYR 0.015 0.001 TYR F 50 PHE 0.025 0.002 PHE A 304 TRP 0.011 0.001 TRP H 70 HIS 0.004 0.001 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (16012) covalent geometry : angle 0.57747 / 0.29 (21783) SS BOND : bond 0.00371 / 0.21 ( 16) SS BOND : angle 0.96484 / 0.50 ( 32) hydrogen bonds : bond 0.03433 / 2.25 ( 622) hydrogen bonds : angle 4.77386 / 3.37 ( 1647) link_ALPHA1-2 : bond 0.00169 / 0.09 ( 1) link_ALPHA1-2 : angle 1.75825 / 0.79 ( 3) link_ALPHA1-3 : bond 0.00245 / 0.12 ( 2) link_ALPHA1-3 : angle 1.66075 / 0.73 ( 6) link_ALPHA1-6 : bond 0.00586 / 0.31 ( 1) link_ALPHA1-6 : angle 1.14195 / 0.55 ( 3) link_BETA1-4 : bond 0.00119 / 0.06 ( 4) link_BETA1-4 : angle 1.83077 / 0.81 ( 12) link_NAG-ASN : bond 0.00217 / 0.13 ( 14) link_NAG-ASN : angle 1.54486 / 0.90 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8598 (tt0) cc_final: 0.8173 (mt0) REVERT: A 88 TYR cc_start: 0.8769 (m-80) cc_final: 0.8441 (m-80) REVERT: A 596 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 619 ASP cc_start: 0.8228 (t0) cc_final: 0.7944 (t0) REVERT: B 54 CYS cc_start: 0.8877 (p) cc_final: 0.8579 (p) REVERT: B 237 GLN cc_start: 0.8749 (mp10) cc_final: 0.8399 (mp10) REVERT: C 197 ASP cc_start: 0.8918 (p0) cc_final: 0.8510 (p0) REVERT: C 215 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: C 366 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 370 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.9036 (m) REVERT: C 377 MET cc_start: 0.8610 (mmp) cc_final: 0.8157 (mmm) REVERT: C 435 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: D 33 ASN cc_start: 0.8618 (t0) cc_final: 0.8216 (t0) REVERT: D 40 GLN cc_start: 0.7706 (pp30) cc_final: 0.7391 (pp30) REVERT: D 43 SER cc_start: 0.8221 (t) cc_final: 0.7922 (t) REVERT: D 58 GLN cc_start: 0.8379 (tp40) cc_final: 0.7785 (tp40) REVERT: D 61 MET cc_start: 0.7401 (mmm) cc_final: 0.7055 (mmp) REVERT: D 74 GLU cc_start: 0.6823 (tt0) cc_final: 0.6568 (tp30) REVERT: D 165 GLU cc_start: 0.8040 (mp0) cc_final: 0.7466 (mp0) REVERT: D 173 ASP cc_start: 0.8571 (t0) cc_final: 0.8080 (t70) REVERT: D 176 GLN cc_start: 0.8646 (mt0) cc_final: 0.8350 (mt0) REVERT: D 196 LYS cc_start: 0.6643 (pttp) cc_final: 0.6214 (mtmm) REVERT: D 215 ASP cc_start: 0.7796 (p0) cc_final: 0.7422 (p0) REVERT: D 306 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7712 (m) REVERT: E 68 LYS cc_start: 0.8334 (ttpt) cc_final: 0.7981 (ttpt) REVERT: F 88 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8387 (mt0) REVERT: F 93 MET cc_start: 0.8815 (mtt) cc_final: 0.8484 (mtt) REVERT: F 104 MET cc_start: 0.8251 (tmm) cc_final: 0.7894 (tmm) REVERT: F 112 GLU cc_start: 0.8640 (pt0) cc_final: 0.8030 (pm20) REVERT: G 70 GLN cc_start: 0.8126 (mt0) cc_final: 0.7832 (mt0) REVERT: G 76 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (mp) REVERT: G 89 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7911 (ptt-90) REVERT: G 107 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5656 (mm-30) REVERT: G 121 GLN cc_start: 0.8106 (mt0) cc_final: 0.7826 (mp10) REVERT: H 66 LYS cc_start: 0.7322 (mppt) cc_final: 0.6928 (mptt) REVERT: H 96 ASP cc_start: 0.8234 (t70) cc_final: 0.7327 (t70) REVERT: H 99 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7173 (mp0) REVERT: H 112 GLU cc_start: 0.7827 (pm20) cc_final: 0.7388 (pm20) outliers start: 42 outliers final: 29 residues processed: 251 average time/residue: 0.6035 time to fit residues: 167.5108 Evaluate side-chains 259 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 121 optimal weight: 0.9990 chunk 129 optimal weight: 0.0470 chunk 133 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.096265 restraints weight = 27176.714| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.71 r_work: 0.3138 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16050 Z= 0.125 Angle : 0.579 11.153 21881 Z= 0.293 Chirality : 0.042 0.210 2557 Planarity : 0.004 0.043 2735 Dihedral : 4.384 23.891 2108 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 17.78 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1887 helix: 1.49 (0.26), residues: 405 sheet: 0.65 (0.23), residues: 486 loop : -0.08 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 41 TYR 0.023 0.001 TYR A 682 PHE 0.024 0.001 PHE A 304 TRP 0.010 0.001 TRP C 330 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (16012) covalent geometry : angle 0.57033 / 0.29 (21783) SS BOND : bond 0.00312 / 0.20 ( 16) SS BOND : angle 1.77553 / 0.93 ( 32) hydrogen bonds : bond 0.03199 / 2.08 ( 622) hydrogen bonds : angle 4.73934 / 3.35 ( 1647) link_ALPHA1-2 : bond 0.00037 / 0.02 ( 1) link_ALPHA1-2 : angle 1.56917 / 0.70 ( 3) link_ALPHA1-3 : bond 0.00338 / 0.17 ( 2) link_ALPHA1-3 : angle 1.55835 / 0.67 ( 6) link_ALPHA1-6 : bond 0.00768 / 0.40 ( 1) link_ALPHA1-6 : angle 1.11538 / 0.54 ( 3) link_BETA1-4 : bond 0.00162 / 0.08 ( 4) link_BETA1-4 : angle 1.72417 / 0.75 ( 12) link_NAG-ASN : bond 0.00158 / 0.09 ( 14) link_NAG-ASN : angle 1.40860 / 0.82 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3774 Ramachandran restraints generated. 1887 Oldfield, 0 Emsley, 1887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8540 (tt0) cc_final: 0.8103 (mt0) REVERT: A 88 TYR cc_start: 0.8719 (m-80) cc_final: 0.8361 (m-80) REVERT: A 596 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8569 (mm) REVERT: A 619 ASP cc_start: 0.8137 (t0) cc_final: 0.7868 (t0) REVERT: B 54 CYS cc_start: 0.8729 (p) cc_final: 0.8396 (p) REVERT: B 237 GLN cc_start: 0.8702 (mp10) cc_final: 0.8346 (mp10) REVERT: C 197 ASP cc_start: 0.8805 (p0) cc_final: 0.8412 (p0) REVERT: C 215 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8185 (mm110) REVERT: C 366 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7880 (mm-30) REVERT: C 370 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9046 (p) REVERT: C 377 MET cc_start: 0.8521 (mmp) cc_final: 0.8010 (mmm) REVERT: D 33 ASN cc_start: 0.8530 (t0) cc_final: 0.8112 (t0) REVERT: D 43 SER cc_start: 0.8036 (t) cc_final: 0.7781 (t) REVERT: D 58 GLN cc_start: 0.8271 (tp40) cc_final: 0.7688 (tp40) REVERT: D 61 MET cc_start: 0.7187 (mmm) cc_final: 0.6858 (mmp) REVERT: D 165 GLU cc_start: 0.7938 (mp0) cc_final: 0.7357 (mp0) REVERT: D 173 ASP cc_start: 0.8430 (t0) cc_final: 0.8227 (t0) REVERT: D 176 GLN cc_start: 0.8534 (mt0) cc_final: 0.8278 (mt0) REVERT: D 215 ASP cc_start: 0.7683 (p0) cc_final: 0.7340 (p0) REVERT: D 306 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7734 (m) REVERT: E 47 ARG cc_start: 0.8272 (ttt90) cc_final: 0.8013 (ttt180) REVERT: E 68 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7859 (ttpt) REVERT: F 88 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8388 (mt0) REVERT: F 93 MET cc_start: 0.8736 (mtt) cc_final: 0.8443 (mtt) REVERT: F 112 GLU cc_start: 0.8493 (pt0) cc_final: 0.7944 (pm20) REVERT: G 70 GLN cc_start: 0.8089 (mt0) cc_final: 0.7768 (mt0) REVERT: G 76 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7749 (mp) REVERT: G 89 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7667 (ptt-90) REVERT: G 107 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5648 (mm-30) REVERT: G 121 GLN cc_start: 0.8032 (mt0) cc_final: 0.7773 (mp10) REVERT: H 66 LYS cc_start: 0.7295 (mppt) cc_final: 0.7013 (mppt) REVERT: H 96 ASP cc_start: 0.8227 (t70) cc_final: 0.7313 (t70) REVERT: H 99 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7121 (mp0) REVERT: H 112 GLU cc_start: 0.7758 (pm20) cc_final: 0.7492 (pm20) outliers start: 43 outliers final: 28 residues processed: 253 average time/residue: 0.5842 time to fit residues: 164.1029 Evaluate side-chains 256 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 692 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 ARG Chi-restraints excluded: chain G residue 102 LYS Chi-restraints excluded: chain G residue 107 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 119 CYS Chi-restraints excluded: chain H residue 145 GLN Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 130 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN F 24 GLN F 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096126 restraints weight = 26991.290| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.70 r_work: 0.3142 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16050 Z= 0.137 Angle : 0.585 11.215 21881 Z= 0.297 Chirality : 0.043 0.216 2557 Planarity : 0.004 0.042 2735 Dihedral : 4.360 21.294 2108 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.34 % Allowed : 18.48 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.19), residues: 1887 helix: 1.47 (0.26), residues: 405 sheet: 0.67 (0.24), residues: 476 loop : -0.11 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 41 TYR 0.013 0.001 TYR F 50 PHE 0.027 0.001 PHE A 304 TRP 0.010 0.001 TRP C 183 HIS 0.003 0.001 HIS F 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (16012) covalent geometry : angle 0.57399 / 0.29 (21783) SS BOND : bond 0.00353 / 0.21 ( 16) SS BOND : angle 2.13775 / 1.12 ( 32) hydrogen bonds : bond 0.03283 / 2.13 ( 622) hydrogen bonds : angle 4.72313 / 3.33 ( 1647) link_ALPHA1-2 : bond 0.00138 / 0.07 ( 1) link_ALPHA1-2 : angle 1.61346 / 0.73 ( 3) link_ALPHA1-3 : bond 0.00289 / 0.14 ( 2) link_ALPHA1-3 : angle 1.60712 / 0.69 ( 6) link_ALPHA1-6 : bond 0.00693 / 0.36 ( 1) link_ALPHA1-6 : angle 1.14917 / 0.56 ( 3) link_BETA1-4 : bond 0.00151 / 0.08 ( 4) link_BETA1-4 : angle 1.76532 / 0.78 ( 12) link_NAG-ASN : bond 0.00156 / 0.09 ( 14) link_NAG-ASN : angle 1.46502 / 0.86 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5494.55 seconds wall clock time: 94 minutes 37.00 seconds (5677.00 seconds total)