Starting phenix.real_space_refine on Tue Jun 24 12:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4r_25686/06_2025/7t4r_25686.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.036 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 145 5.16 5 C 18240 2.51 5 N 4934 2.21 5 O 5398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28717 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1083 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 1 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5075 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 598} Chain breaks: 6 Chain: "C" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1843 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 213} Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1038 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1327 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 152} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 900 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 782 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Chain: "I" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: "K" Number of atoms: 5097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5097 Classifications: {'peptide': 633} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 601} Chain breaks: 6 Chain: "L" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1818 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 211} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1067 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 1 Chain: "N" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 152} Chain: "O" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 869 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "P" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 782 Classifications: {'peptide': 104} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 96} Chain: "R" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "S" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 988 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N GLU D 136 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU D 136 " occ=0.97 residue: pdb=" N ASP D 138 " occ=0.99 ... (6 atoms not shown) pdb=" OD2 ASP D 138 " occ=0.99 residue: pdb=" N GLU M 136 " occ=0.97 ... (7 atoms not shown) pdb=" OE2 GLU M 136 " occ=0.97 Time building chain proxies: 17.96, per 1000 atoms: 0.63 Number of scatterers: 28717 At special positions: 0 Unit cell: (217.738, 113.696, 225.246, 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 145 16.00 O 5398 8.00 N 4934 7.00 C 18240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 35 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS C 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 383 " distance=2.04 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 624 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 207 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 116 " distance=2.04 Simple disulfide: pdb=" SG CYS J 45 " - pdb=" SG CYS J 119 " distance=2.04 Simple disulfide: pdb=" SG CYS K 59 " - pdb=" SG CYS L 54 " distance=2.03 Simple disulfide: pdb=" SG CYS K 95 " - pdb=" SG CYS L 47 " distance=2.03 Simple disulfide: pdb=" SG CYS K 195 " - pdb=" SG CYS K 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 330 " - pdb=" SG CYS K 383 " distance=2.04 Simple disulfide: pdb=" SG CYS K 495 " - pdb=" SG CYS K 522 " distance=2.03 Simple disulfide: pdb=" SG CYS K 571 " - pdb=" SG CYS K 624 " distance=2.03 Simple disulfide: pdb=" SG CYS L 144 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 96 " - pdb=" SG CYS M 111 " distance=2.03 Simple disulfide: pdb=" SG CYS N 172 " - pdb=" SG CYS N 207 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 116 " distance=2.04 Simple disulfide: pdb=" SG CYS S 45 " - pdb=" SG CYS S 119 " distance=2.04 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 NAG-ASN " NAG B 802 " - " ASN B 62 " " NAG B 803 " - " ASN B 67 " " NAG B 804 " - " ASN B 192 " " NAG B 805 " - " ASN B 700 " " NAG C 301 " - " ASN C 74 " " NAG E 301 " - " ASN E 201 " " NAG K 802 " - " ASN K 67 " " NAG K 803 " - " ASN K 192 " " NAG K 804 " - " ASN K 700 " " NAG N 301 " - " ASN N 201 " " NAG O 201 " - " ASN O 81 " Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 3.5 seconds 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6788 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 42 sheets defined 30.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N LEU B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 4.186A pdb=" N PHE B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.703A pdb=" N LEU B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 334 through 352 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.907A pdb=" N GLY B 358 " --> pdb=" O GLN B 354 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 362 through 385 Processing helix chain 'B' and resid 396 through 409 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.627A pdb=" N LEU B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.599A pdb=" N ILE B 435 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 454 removed outlier: 3.695A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 447 " --> pdb=" O ILE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.658A pdb=" N HIS B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 494 removed outlier: 3.633A pdb=" N LEU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 Processing helix chain 'B' and resid 514 through 519 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 671 through 680 Processing helix chain 'B' and resid 681 through 684 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.744A pdb=" N VAL C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.889A pdb=" N TRP C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 172 through 176 removed outlier: 4.223A pdb=" N THR C 175 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 236 removed outlier: 4.098A pdb=" N PHE C 222 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 252 removed outlier: 4.124A pdb=" N HIS C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'D' and resid 76 through 84 removed outlier: 4.030A pdb=" N THR D 81 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS D 82 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 92 through 97 removed outlier: 7.125A pdb=" N SER D 95 " --> pdb=" O LYS D 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN D 97 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.672A pdb=" N CYS E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 57' Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.653A pdb=" N GLY E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 117 " --> pdb=" O TYR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 130 removed outlier: 3.920A pdb=" N GLN E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'F' and resid 22 through 27 removed outlier: 3.927A pdb=" N LYS F 27 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 41 Processing helix chain 'F' and resid 45 through 69 Processing helix chain 'F' and resid 76 through 80 removed outlier: 3.537A pdb=" N ARG F 79 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.922A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 107 through 111 removed outlier: 3.520A pdb=" N VAL I 111 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'K' and resid 93 through 98 removed outlier: 3.583A pdb=" N LEU K 96 " --> pdb=" O PRO K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 109 removed outlier: 3.550A pdb=" N GLU K 103 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE K 105 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN K 108 " --> pdb=" O GLN K 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL K 109 " --> pdb=" O PHE K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 122 removed outlier: 3.526A pdb=" N LEU K 122 " --> pdb=" O TYR K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 264 through 266 No H-bonds generated for 'chain 'K' and resid 264 through 266' Processing helix chain 'K' and resid 282 through 286 Processing helix chain 'K' and resid 289 through 294 Processing helix chain 'K' and resid 298 through 303 Processing helix chain 'K' and resid 308 through 316 Processing helix chain 'K' and resid 316 through 328 Processing helix chain 'K' and resid 334 through 352 Processing helix chain 'K' and resid 354 through 359 removed outlier: 3.848A pdb=" N GLY K 358 " --> pdb=" O GLN K 354 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 359 " --> pdb=" O GLU K 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 354 through 359' Processing helix chain 'K' and resid 362 through 385 Processing helix chain 'K' and resid 396 through 409 Processing helix chain 'K' and resid 415 through 429 removed outlier: 3.614A pdb=" N LEU K 419 " --> pdb=" O ASP K 415 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG K 421 " --> pdb=" O THR K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 435 Processing helix chain 'K' and resid 436 through 454 removed outlier: 3.785A pdb=" N LEU K 440 " --> pdb=" O PRO K 436 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA K 447 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS K 454 " --> pdb=" O LEU K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.752A pdb=" N LEU K 469 " --> pdb=" O GLN K 465 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL K 474 " --> pdb=" O MET K 470 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS K 475 " --> pdb=" O GLY K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 494 removed outlier: 3.708A pdb=" N LEU K 494 " --> pdb=" O VAL K 490 " (cutoff:3.500A) Processing helix chain 'K' and resid 496 through 507 Processing helix chain 'K' and resid 514 through 519 Processing helix chain 'K' and resid 520 through 524 Processing helix chain 'K' and resid 531 through 537 Processing helix chain 'K' and resid 547 through 559 removed outlier: 3.600A pdb=" N GLN K 559 " --> pdb=" O LEU K 555 " (cutoff:3.500A) Processing helix chain 'K' and resid 671 through 680 Processing helix chain 'K' and resid 681 through 684 Processing helix chain 'L' and resid 46 through 57 removed outlier: 3.613A pdb=" N GLY L 57 " --> pdb=" O ARG L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 70 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.687A pdb=" N VAL L 99 " --> pdb=" O ALA L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 113 Processing helix chain 'L' and resid 117 through 127 Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.993A pdb=" N TRP L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 167 No H-bonds generated for 'chain 'L' and resid 165 through 167' Processing helix chain 'L' and resid 215 through 217 No H-bonds generated for 'chain 'L' and resid 215 through 217' Processing helix chain 'L' and resid 218 through 236 removed outlier: 4.108A pdb=" N PHE L 222 " --> pdb=" O GLY L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 252 removed outlier: 3.777A pdb=" N HIS L 245 " --> pdb=" O PRO L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 258 Processing helix chain 'M' and resid 71 through 79 removed outlier: 4.092A pdb=" N GLY M 75 " --> pdb=" O ALA M 71 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 3.754A pdb=" N LEU M 93 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 97 Processing helix chain 'M' and resid 117 through 119 No H-bonds generated for 'chain 'M' and resid 117 through 119' Processing helix chain 'M' and resid 145 through 157 Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 80 through 84 Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.818A pdb=" N GLY N 116 " --> pdb=" O TRP N 112 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG N 117 " --> pdb=" O TYR N 113 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN N 118 " --> pdb=" O LEU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 130 removed outlier: 3.722A pdb=" N GLN N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Proline residue: N 126 - end of helix Processing helix chain 'N' and resid 140 through 151 Processing helix chain 'O' and resid 23 through 27 removed outlier: 3.840A pdb=" N LYS O 27 " --> pdb=" O THR O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 41 Processing helix chain 'O' and resid 45 through 69 Processing helix chain 'O' and resid 73 through 78 removed outlier: 4.250A pdb=" N LEU O 77 " --> pdb=" O ASN O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 95 Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.122A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 65 Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 107 through 111 Processing helix chain 'S' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.885A pdb=" N GLY A 27 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 85 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 166 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP A 87 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLU A 168 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLY A 89 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 14.844A pdb=" N HIS A 170 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 21.479A pdb=" N GLN A 91 " --> pdb=" O HIS A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.599A pdb=" N ARG A 85 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 166 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP A 87 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLU A 168 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N GLY A 89 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 14.844A pdb=" N HIS A 170 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 21.479A pdb=" N GLN A 91 " --> pdb=" O HIS A 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 88 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL A 138 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU A 90 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 136 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 92 removed outlier: 6.564A pdb=" N SER B 77 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU C 183 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN B 79 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 178 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA C 194 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 189 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 138 removed outlier: 5.815A pdb=" N ILE B 268 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 279 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 270 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 233 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 581 Processing sheet with id=AA7, first strand: chain 'B' and resid 637 through 638 removed outlier: 7.000A pdb=" N THR B 637 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 155 removed outlier: 5.308A pdb=" N GLY C 161 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 54 through 57 Processing sheet with id=AB1, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AB2, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AB3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.807A pdb=" N GLU G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.807A pdb=" N GLU G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP G 112 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.657A pdb=" N ALA H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.459A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AB9, first strand: chain 'I' and resid 33 through 35 removed outlier: 3.525A pdb=" N ILE I 76 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL I 65 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU I 74 " --> pdb=" O VAL I 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 26 through 30 Processing sheet with id=AC2, first strand: chain 'J' and resid 33 through 34 removed outlier: 6.334A pdb=" N GLY J 33 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER J 56 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL J 57 " --> pdb=" O SER J 73 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER J 73 " --> pdb=" O VAL J 57 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP J 59 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 33 through 34 removed outlier: 6.334A pdb=" N GLY J 33 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL J 142 " --> pdb=" O ARG J 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 50 through 51 removed outlier: 6.671A pdb=" N ARG K 50 " --> pdb=" O VAL K 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'K' and resid 65 through 66 removed outlier: 6.021A pdb=" N VAL L 178 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA L 194 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE L 189 " --> pdb=" O VAL L 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 204 " --> pdb=" O ILE L 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 136 through 138 removed outlier: 3.798A pdb=" N ARG K 136 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU K 277 " --> pdb=" O LEU K 269 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG K 223 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 194 through 197 Processing sheet with id=AC8, first strand: chain 'K' and resid 579 through 581 Processing sheet with id=AC9, first strand: chain 'K' and resid 637 through 638 removed outlier: 7.082A pdb=" N THR K 637 " --> pdb=" O GLU K 705 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER K 652 " --> pdb=" O TYR K 668 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR K 668 " --> pdb=" O SER K 652 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU K 654 " --> pdb=" O ILE K 666 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE K 666 " --> pdb=" O LEU K 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU K 656 " --> pdb=" O ILE K 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 150 through 155 removed outlier: 5.129A pdb=" N GLY L 161 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU N 88 " --> pdb=" O ARG N 76 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG N 76 " --> pdb=" O LEU N 88 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU N 90 " --> pdb=" O PHE N 74 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE N 74 " --> pdb=" O LEU N 90 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR N 92 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 45 through 50 removed outlier: 3.507A pdb=" N ASP M 45 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS M 49 " --> pdb=" O THR M 53 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR M 53 " --> pdb=" O CYS M 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'M' and resid 130 through 132 Processing sheet with id=AD5, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.463A pdb=" N GLU P 10 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE P 34 " --> pdb=" O ILE P 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 10 through 11 removed outlier: 6.463A pdb=" N GLU P 10 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP P 112 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AD9, first strand: chain 'Q' and resid 45 through 46 Processing sheet with id=AE1, first strand: chain 'R' and resid 27 through 29 Processing sheet with id=AE2, first strand: chain 'R' and resid 33 through 35 removed outlier: 3.691A pdb=" N GLU R 133 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE R 76 " --> pdb=" O TRP R 63 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL R 65 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU R 74 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 33 through 35 removed outlier: 3.691A pdb=" N GLU R 133 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN R 118 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR R 125 " --> pdb=" O GLN R 118 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 26 through 30 Processing sheet with id=AE5, first strand: chain 'S' and resid 33 through 34 removed outlier: 4.259A pdb=" N SER S 56 " --> pdb=" O ASP S 122 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL S 57 " --> pdb=" O SER S 73 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER S 73 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP S 59 " --> pdb=" O VAL S 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 33 through 34 removed outlier: 4.037A pdb=" N VAL S 142 " --> pdb=" O ARG S 121 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3069 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: 13.45 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9308 1.34 - 1.47: 7292 1.47 - 1.59: 12577 1.59 - 1.72: 0 1.72 - 1.85: 204 Bond restraints: 29381 Sorted by residual: bond pdb=" N SER H 7 " pdb=" CA SER H 7 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.18e-02 7.18e+03 9.23e+00 bond pdb=" N CYS E 83 " pdb=" CA CYS E 83 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.45e+00 bond pdb=" N HIS E 150 " pdb=" CA HIS E 150 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.27e-02 6.20e+03 8.15e+00 bond pdb=" N GLU E 82 " pdb=" CA GLU E 82 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.63e+00 bond pdb=" N GLN P 6 " pdb=" CA GLN P 6 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.52e+00 ... (remaining 29376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 38383 1.48 - 2.95: 1258 2.95 - 4.43: 260 4.43 - 5.91: 22 5.91 - 7.38: 8 Bond angle restraints: 39931 Sorted by residual: angle pdb=" C GLY E 80 " pdb=" N PRO E 81 " pdb=" CA PRO E 81 " ideal model delta sigma weight residual 119.28 123.95 -4.67 1.10e+00 8.26e-01 1.81e+01 angle pdb=" C ARG E 76 " pdb=" N VAL E 77 " pdb=" CA VAL E 77 " ideal model delta sigma weight residual 123.11 117.31 5.80 1.38e+00 5.25e-01 1.77e+01 angle pdb=" CA GLY E 80 " pdb=" C GLY E 80 " pdb=" O GLY E 80 " ideal model delta sigma weight residual 122.46 118.97 3.49 9.70e-01 1.06e+00 1.29e+01 angle pdb=" CA TYR C 162 " pdb=" CB TYR C 162 " pdb=" CG TYR C 162 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" N THR E 208 " pdb=" CA THR E 208 " pdb=" C THR E 208 " ideal model delta sigma weight residual 112.45 107.74 4.71 1.39e+00 5.18e-01 1.15e+01 ... (remaining 39926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 16380 17.81 - 35.62: 1149 35.62 - 53.43: 216 53.43 - 71.24: 50 71.24 - 89.05: 27 Dihedral angle restraints: 17822 sinusoidal: 7287 harmonic: 10535 Sorted by residual: dihedral pdb=" CB CYS K 59 " pdb=" SG CYS K 59 " pdb=" SG CYS L 54 " pdb=" CB CYS L 54 " ideal model delta sinusoidal sigma weight residual -86.00 -159.51 73.51 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS J 45 " pdb=" SG CYS J 45 " pdb=" SG CYS J 119 " pdb=" CB CYS J 119 " ideal model delta sinusoidal sigma weight residual 93.00 166.39 -73.39 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS B 59 " pdb=" SG CYS B 59 " pdb=" SG CYS C 54 " pdb=" CB CYS C 54 " ideal model delta sinusoidal sigma weight residual -86.00 -148.51 62.51 1 1.00e+01 1.00e-02 5.17e+01 ... (remaining 17819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3694 0.053 - 0.105: 658 0.105 - 0.158: 169 0.158 - 0.211: 4 0.211 - 0.263: 2 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG B 803 " pdb=" ND2 ASN B 67 " pdb=" C2 NAG B 803 " pdb=" O5 NAG B 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 74 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG K 802 " pdb=" ND2 ASN K 67 " pdb=" C2 NAG K 802 " pdb=" O5 NAG K 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 4524 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 67 " 0.049 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO E 68 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 68 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 68 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 171 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO A 172 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 226 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C TYR C 226 " 0.048 2.00e-02 2.50e+03 pdb=" O TYR C 226 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN C 227 " -0.016 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 591 2.68 - 3.23: 28575 3.23 - 3.79: 42239 3.79 - 4.34: 59147 4.34 - 4.90: 98485 Nonbonded interactions: 229037 Sorted by model distance: nonbonded pdb=" O3 NAG K 802 " pdb=" O7 NAG K 802 " model vdw 2.123 3.040 nonbonded pdb=" O VAL B 256 " pdb=" NH2 ARG B 264 " model vdw 2.196 3.120 nonbonded pdb=" O ARG C 133 " pdb=" OG1 THR C 136 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 114 " pdb=" OE1 GLU B 116 " model vdw 2.221 3.040 nonbonded pdb=" O TYR K 84 " pdb=" OD1 ASN K 85 " model vdw 2.225 3.040 ... (remaining 229032 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 'B' and (resid 42 through 539 or resid 543 through 641 or resid 644 throu \ gh 709 or resid 801 through 805)) selection = (chain 'K' and (resid 42 through 169 or resid 183 through 657 or resid 663 throu \ gh 709 or resid 801 through 805)) } ncs_group { reference = (chain 'C' and resid 44 through 273) selection = chain 'L' } ncs_group { reference = (chain 'D' and (resid 36 through 103 or resid 109 through 164)) selection = (chain 'M' and resid 36 through 164) } ncs_group { reference = (chain 'E' and (resid 52 through 213 or resid 301)) selection = (chain 'N' and (resid 52 through 213 or resid 301)) } ncs_group { reference = (chain 'F' and resid 23 through 127) selection = (chain 'O' and resid 23 through 127) } ncs_group { reference = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'J' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 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: 22.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 68.950 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.004 0.070 29421 Z= 0.192 Angle : 0.654 9.137 40022 Z= 0.356 Chirality : 0.044 0.263 4527 Planarity : 0.006 0.075 5105 Dihedral : 13.149 89.046 10947 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3529 helix: -0.54 (0.17), residues: 843 sheet: 0.01 (0.17), residues: 870 loop : -0.55 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 167 HIS 0.011 0.001 HIS B 91 PHE 0.021 0.002 PHE K 234 TYR 0.019 0.002 TYR Q 49 ARG 0.013 0.001 ARG M 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 11) link_NAG-ASN : angle 2.89846 ( 33) hydrogen bonds : bond 0.15362 ( 1169) hydrogen bonds : angle 6.75134 ( 3069) SS BOND : bond 0.00618 ( 29) SS BOND : angle 2.32492 ( 58) covalent geometry : bond 0.00406 (29381) covalent geometry : angle 0.64373 (39931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 150 GLU cc_start: 0.6473 (pp20) cc_final: 0.6114 (tm-30) REVERT: B 304 PHE cc_start: 0.7578 (t80) cc_final: 0.6987 (t80) REVERT: B 319 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6941 (ttt90) REVERT: B 380 MET cc_start: 0.7569 (mmm) cc_final: 0.7290 (mmm) REVERT: B 401 ASP cc_start: 0.7283 (m-30) cc_final: 0.6911 (m-30) REVERT: B 405 ARG cc_start: 0.7549 (mtp180) cc_final: 0.7273 (mtm110) REVERT: B 489 ILE cc_start: 0.8102 (tp) cc_final: 0.7871 (tp) REVERT: B 511 HIS cc_start: 0.6857 (p90) cc_final: 0.6624 (p-80) REVERT: B 577 SER cc_start: 0.8262 (p) cc_final: 0.8057 (p) REVERT: C 113 TYR cc_start: 0.7828 (t80) cc_final: 0.7590 (t80) REVERT: E 117 ARG cc_start: 0.7165 (mtm180) cc_final: 0.6595 (mtm110) REVERT: E 119 GLN cc_start: 0.6767 (pt0) cc_final: 0.6496 (pt0) REVERT: G 31 ASN cc_start: 0.8507 (t0) cc_final: 0.8234 (t0) REVERT: G 91 THR cc_start: 0.8228 (m) cc_final: 0.8004 (p) REVERT: K 489 ILE cc_start: 0.8461 (tp) cc_final: 0.8229 (tt) REVERT: K 519 TYR cc_start: 0.7466 (t80) cc_final: 0.7260 (t80) REVERT: O 122 PHE cc_start: 0.5706 (p90) cc_final: 0.5291 (p90) REVERT: P 2 VAL cc_start: 0.6730 (p) cc_final: 0.6284 (t) REVERT: P 31 ASN cc_start: 0.8197 (t0) cc_final: 0.7879 (t0) REVERT: P 71 THR cc_start: 0.7269 (m) cc_final: 0.6983 (p) REVERT: R 58 TYR cc_start: 0.7974 (m-80) cc_final: 0.7676 (m-80) REVERT: R 64 TYR cc_start: 0.5908 (m-80) cc_final: 0.5707 (m-80) REVERT: R 125 THR cc_start: 0.6797 (p) cc_final: 0.6559 (p) REVERT: S 77 ASP cc_start: 0.8270 (p0) cc_final: 0.8062 (p0) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.4931 time to fit residues: 451.8930 Evaluate side-chains 525 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 0.8980 chunk 267 optimal weight: 0.0980 chunk 148 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 205 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 236 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 38 GLN I 59 ASN ** M 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 HIS ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 ASN Q 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.124574 restraints weight = 51286.538| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.49 r_work: 0.3590 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29421 Z= 0.200 Angle : 0.695 11.332 40022 Z= 0.359 Chirality : 0.047 0.285 4527 Planarity : 0.006 0.067 5105 Dihedral : 6.186 56.168 4268 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.39 % Allowed : 6.55 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3529 helix: -0.11 (0.17), residues: 852 sheet: 0.14 (0.17), residues: 905 loop : -0.24 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 167 HIS 0.008 0.002 HIS B 454 PHE 0.030 0.003 PHE A 108 TYR 0.022 0.002 TYR Q 49 ARG 0.008 0.001 ARG M 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 11) link_NAG-ASN : angle 3.49954 ( 33) hydrogen bonds : bond 0.04916 ( 1169) hydrogen bonds : angle 5.54371 ( 3069) SS BOND : bond 0.00581 ( 29) SS BOND : angle 1.75937 ( 58) covalent geometry : bond 0.00470 (29381) covalent geometry : angle 0.68475 (39931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 549 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7536 (t0) cc_final: 0.7278 (t0) REVERT: B 150 GLU cc_start: 0.7441 (pp20) cc_final: 0.6754 (tm-30) REVERT: B 304 PHE cc_start: 0.8187 (t80) cc_final: 0.7561 (t80) REVERT: B 314 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6697 (mtp85) REVERT: B 319 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7514 (ttt90) REVERT: B 368 ASP cc_start: 0.7308 (t0) cc_final: 0.7073 (t0) REVERT: B 401 ASP cc_start: 0.7430 (m-30) cc_final: 0.7140 (m-30) REVERT: B 489 ILE cc_start: 0.8482 (tp) cc_final: 0.8238 (tp) REVERT: B 511 HIS cc_start: 0.7254 (p90) cc_final: 0.6997 (p-80) REVERT: B 554 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7734 (mp) REVERT: E 79 THR cc_start: 0.7582 (m) cc_final: 0.7061 (p) REVERT: E 117 ARG cc_start: 0.7436 (mtm180) cc_final: 0.6750 (mtm110) REVERT: E 119 GLN cc_start: 0.7117 (pt0) cc_final: 0.6752 (pt0) REVERT: G 31 ASN cc_start: 0.8616 (t0) cc_final: 0.8320 (t0) REVERT: G 81 MET cc_start: 0.6598 (tmm) cc_final: 0.5981 (tmm) REVERT: H 53 THR cc_start: 0.8004 (m) cc_final: 0.7745 (p) REVERT: J 75 ASN cc_start: 0.6966 (p0) cc_final: 0.6693 (p0) REVERT: K 80 PHE cc_start: 0.7583 (m-10) cc_final: 0.7315 (m-10) REVERT: K 589 TYR cc_start: 0.8019 (m-80) cc_final: 0.7807 (m-80) REVERT: N 92 TYR cc_start: 0.8444 (m-80) cc_final: 0.8213 (m-80) REVERT: O 122 PHE cc_start: 0.6232 (p90) cc_final: 0.5506 (p90) REVERT: P 31 ASN cc_start: 0.8530 (t0) cc_final: 0.8287 (t0) outliers start: 44 outliers final: 28 residues processed: 561 average time/residue: 0.5259 time to fit residues: 458.2107 Evaluate side-chains 534 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 504 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 137 SER Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 27 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 136 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 344 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 332 optimal weight: 0.4980 chunk 191 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN K 145 GLN L 245 HIS ** M 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 GLN ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.149651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122058 restraints weight = 51576.660| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.49 r_work: 0.3561 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29421 Z= 0.205 Angle : 0.667 11.209 40022 Z= 0.344 Chirality : 0.046 0.262 4527 Planarity : 0.005 0.064 5105 Dihedral : 5.911 55.771 4268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.28 % Allowed : 9.46 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3529 helix: 0.08 (0.17), residues: 840 sheet: 0.26 (0.17), residues: 860 loop : -0.28 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 106 HIS 0.007 0.001 HIS P 52 PHE 0.026 0.002 PHE K 234 TYR 0.025 0.002 TYR Q 49 ARG 0.008 0.001 ARG E 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 11) link_NAG-ASN : angle 3.07610 ( 33) hydrogen bonds : bond 0.04664 ( 1169) hydrogen bonds : angle 5.33922 ( 3069) SS BOND : bond 0.00573 ( 29) SS BOND : angle 1.67074 ( 58) covalent geometry : bond 0.00484 (29381) covalent geometry : angle 0.65908 (39931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 523 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7213 (t0) cc_final: 0.6971 (t0) REVERT: B 120 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7612 (pp30) REVERT: B 150 GLU cc_start: 0.7047 (pp20) cc_final: 0.6359 (tm-30) REVERT: B 304 PHE cc_start: 0.7984 (t80) cc_final: 0.7450 (t80) REVERT: B 319 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7333 (ttt90) REVERT: B 368 ASP cc_start: 0.7039 (t0) cc_final: 0.6796 (t0) REVERT: B 401 ASP cc_start: 0.7308 (m-30) cc_final: 0.6970 (m-30) REVERT: B 489 ILE cc_start: 0.8387 (tp) cc_final: 0.8135 (tp) REVERT: B 554 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7524 (mp) REVERT: C 70 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.7333 (mmm160) REVERT: C 113 TYR cc_start: 0.8121 (t80) cc_final: 0.7786 (t80) REVERT: E 117 ARG cc_start: 0.7367 (mtm180) cc_final: 0.6759 (mtm110) REVERT: G 31 ASN cc_start: 0.8550 (t0) cc_final: 0.8321 (t0) REVERT: G 36 TRP cc_start: 0.7557 (m100) cc_final: 0.7340 (m-10) REVERT: J 75 ASN cc_start: 0.6779 (p0) cc_final: 0.6528 (p0) REVERT: J 137 TYR cc_start: 0.7975 (t80) cc_final: 0.7610 (t80) REVERT: K 80 PHE cc_start: 0.7496 (m-10) cc_final: 0.7202 (m-10) REVERT: K 193 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7956 (mp10) REVERT: K 533 GLU cc_start: 0.8329 (mp0) cc_final: 0.7737 (pm20) REVERT: K 634 HIS cc_start: 0.7679 (m90) cc_final: 0.7476 (m170) REVERT: N 151 MET cc_start: 0.7434 (mpp) cc_final: 0.7054 (mmm) REVERT: N 206 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.5374 (m-80) REVERT: P 28 THR cc_start: 0.7154 (OUTLIER) cc_final: 0.6920 (p) outliers start: 72 outliers final: 48 residues processed: 554 average time/residue: 0.4415 time to fit residues: 382.3139 Evaluate side-chains 548 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 497 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 564 GLU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 552 LEU Chi-restraints excluded: chain K residue 584 SER Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 127 SER Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 189 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 334 optimal weight: 0.4980 chunk 203 optimal weight: 0.0770 chunk 129 optimal weight: 0.0050 chunk 273 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN K 145 GLN ** M 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 GLN ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.152198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125478 restraints weight = 52030.396| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.55 r_work: 0.3601 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29421 Z= 0.115 Angle : 0.596 19.391 40022 Z= 0.303 Chirality : 0.043 0.257 4527 Planarity : 0.005 0.058 5105 Dihedral : 5.443 55.713 4268 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.02 % Allowed : 11.45 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3529 helix: 0.45 (0.17), residues: 840 sheet: 0.39 (0.17), residues: 854 loop : -0.09 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 134 HIS 0.009 0.001 HIS B 511 PHE 0.034 0.002 PHE O 122 TYR 0.017 0.001 TYR H 87 ARG 0.007 0.000 ARG E 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 11) link_NAG-ASN : angle 4.57130 ( 33) hydrogen bonds : bond 0.03700 ( 1169) hydrogen bonds : angle 5.00357 ( 3069) SS BOND : bond 0.00533 ( 29) SS BOND : angle 1.33598 ( 58) covalent geometry : bond 0.00259 (29381) covalent geometry : angle 0.57942 (39931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 525 time to evaluate : 2.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7304 (t0) cc_final: 0.7059 (t0) REVERT: B 150 GLU cc_start: 0.7092 (pp20) cc_final: 0.6412 (tm-30) REVERT: B 304 PHE cc_start: 0.7959 (t80) cc_final: 0.7419 (t80) REVERT: B 319 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7228 (ttt90) REVERT: B 368 ASP cc_start: 0.7033 (t0) cc_final: 0.6784 (t0) REVERT: B 401 ASP cc_start: 0.7292 (m-30) cc_final: 0.6928 (m-30) REVERT: B 473 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 554 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7539 (mp) REVERT: B 562 THR cc_start: 0.8709 (t) cc_final: 0.8348 (m) REVERT: C 60 PHE cc_start: 0.7632 (m-80) cc_final: 0.7256 (m-10) REVERT: C 70 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7267 (mmm160) REVERT: C 113 TYR cc_start: 0.8120 (t80) cc_final: 0.7838 (t80) REVERT: D 76 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6727 (mt) REVERT: G 31 ASN cc_start: 0.8449 (t0) cc_final: 0.8187 (t0) REVERT: G 36 TRP cc_start: 0.7455 (m100) cc_final: 0.7242 (m-10) REVERT: J 137 TYR cc_start: 0.7969 (t80) cc_final: 0.7499 (t80) REVERT: K 193 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7932 (mp10) REVERT: L 112 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7920 (mp) REVERT: L 239 ASP cc_start: 0.8422 (t0) cc_final: 0.7883 (t0) REVERT: L 247 ASP cc_start: 0.7591 (m-30) cc_final: 0.7360 (m-30) REVERT: M 120 TYR cc_start: 0.8113 (m-80) cc_final: 0.7675 (m-80) REVERT: N 151 MET cc_start: 0.7357 (mpp) cc_final: 0.6955 (mmm) REVERT: P 28 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.6791 (p) REVERT: P 100 PHE cc_start: 0.6973 (t80) cc_final: 0.6764 (t80) outliers start: 64 outliers final: 33 residues processed: 557 average time/residue: 0.4302 time to fit residues: 371.4099 Evaluate side-chains 541 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 503 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 191 GLN Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain Q residue 27 GLN Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 278 optimal weight: 0.0770 chunk 200 optimal weight: 0.5980 chunk 76 optimal weight: 0.0670 chunk 169 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 165 optimal weight: 0.9980 chunk 325 optimal weight: 5.9990 chunk 134 optimal weight: 0.0980 chunk 251 optimal weight: 2.9990 chunk 258 optimal weight: 0.0020 chunk 120 optimal weight: 6.9990 overall best weight: 0.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN K 318 HIS K 370 GLN M 99 ASN ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127722 restraints weight = 51759.727| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.45 r_work: 0.3640 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29421 Z= 0.103 Angle : 0.568 14.596 40022 Z= 0.288 Chirality : 0.042 0.247 4527 Planarity : 0.004 0.053 5105 Dihedral : 5.126 55.735 4268 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.90 % Allowed : 12.18 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3529 helix: 0.73 (0.18), residues: 840 sheet: 0.59 (0.18), residues: 834 loop : -0.01 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 134 HIS 0.007 0.001 HIS L 236 PHE 0.041 0.001 PHE F 122 TYR 0.023 0.001 TYR D 65 ARG 0.010 0.000 ARG K 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 11) link_NAG-ASN : angle 3.72104 ( 33) hydrogen bonds : bond 0.03349 ( 1169) hydrogen bonds : angle 4.78105 ( 3069) SS BOND : bond 0.00344 ( 29) SS BOND : angle 1.23862 ( 58) covalent geometry : bond 0.00225 (29381) covalent geometry : angle 0.55681 (39931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 521 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7287 (t0) cc_final: 0.7033 (t0) REVERT: B 150 GLU cc_start: 0.6908 (pp20) cc_final: 0.6238 (tm-30) REVERT: B 319 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7138 (ttt90) REVERT: B 368 ASP cc_start: 0.6961 (t0) cc_final: 0.6705 (t0) REVERT: B 401 ASP cc_start: 0.7220 (m-30) cc_final: 0.6881 (m-30) REVERT: B 473 LEU cc_start: 0.8104 (tt) cc_final: 0.7493 (tp) REVERT: B 554 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 562 THR cc_start: 0.8497 (t) cc_final: 0.8239 (m) REVERT: C 60 PHE cc_start: 0.7497 (m-80) cc_final: 0.7171 (m-10) REVERT: C 70 ARG cc_start: 0.7470 (mmm-85) cc_final: 0.7259 (mmm160) REVERT: C 113 TYR cc_start: 0.8277 (t80) cc_final: 0.8020 (t80) REVERT: C 156 ASP cc_start: 0.7305 (t0) cc_final: 0.7031 (t0) REVERT: C 239 ASP cc_start: 0.6716 (t0) cc_final: 0.6298 (t0) REVERT: C 244 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7386 (mmt180) REVERT: E 122 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7325 (mp) REVERT: G 31 ASN cc_start: 0.8393 (t0) cc_final: 0.8122 (t0) REVERT: G 36 TRP cc_start: 0.7356 (m100) cc_final: 0.7123 (m-10) REVERT: J 137 TYR cc_start: 0.7978 (t80) cc_final: 0.7459 (t80) REVERT: K 145 GLN cc_start: 0.8310 (mp10) cc_final: 0.8101 (pm20) REVERT: K 499 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: L 68 TRP cc_start: 0.7783 (p90) cc_final: 0.7570 (p90) REVERT: L 112 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8029 (mp) REVERT: L 125 LEU cc_start: 0.7900 (mt) cc_final: 0.7700 (mt) REVERT: M 120 TYR cc_start: 0.8090 (m-80) cc_final: 0.7784 (m-80) REVERT: N 151 MET cc_start: 0.7363 (mpp) cc_final: 0.6919 (mmm) REVERT: N 202 GLN cc_start: 0.7252 (mt0) cc_final: 0.6865 (mt0) REVERT: O 122 PHE cc_start: 0.5578 (p90) cc_final: 0.4766 (p90) REVERT: P 28 THR cc_start: 0.6988 (OUTLIER) cc_final: 0.6742 (p) REVERT: Q 4 MET cc_start: 0.6616 (mtp) cc_final: 0.6328 (mtp) REVERT: R 64 TYR cc_start: 0.5402 (m-80) cc_final: 0.3816 (m-80) REVERT: S 106 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7324 (ppp) outliers start: 60 outliers final: 37 residues processed: 552 average time/residue: 0.4359 time to fit residues: 375.6993 Evaluate side-chains 537 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 494 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 499 GLU Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 166 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN ** K 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 HIS ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.149102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121509 restraints weight = 51833.877| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.59 r_work: 0.3543 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29421 Z= 0.233 Angle : 0.666 12.168 40022 Z= 0.341 Chirality : 0.046 0.239 4527 Planarity : 0.005 0.056 5105 Dihedral : 5.506 55.640 4268 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.56 % Allowed : 12.65 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3529 helix: 0.30 (0.17), residues: 830 sheet: 0.39 (0.18), residues: 850 loop : -0.19 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 113 HIS 0.011 0.002 HIS B 165 PHE 0.031 0.003 PHE K 234 TYR 0.031 0.002 TYR Q 49 ARG 0.011 0.001 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 11) link_NAG-ASN : angle 3.35297 ( 33) hydrogen bonds : bond 0.04524 ( 1169) hydrogen bonds : angle 5.07552 ( 3069) SS BOND : bond 0.00591 ( 29) SS BOND : angle 1.75352 ( 58) covalent geometry : bond 0.00556 (29381) covalent geometry : angle 0.65642 (39931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 495 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7686 (t0) cc_final: 0.7425 (t0) REVERT: B 150 GLU cc_start: 0.7322 (pp20) cc_final: 0.6526 (tm-30) REVERT: B 304 PHE cc_start: 0.8331 (t80) cc_final: 0.7878 (t80) REVERT: B 319 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7491 (ttt90) REVERT: B 368 ASP cc_start: 0.7498 (t0) cc_final: 0.7219 (t0) REVERT: B 401 ASP cc_start: 0.7515 (m-30) cc_final: 0.7177 (m-30) REVERT: B 554 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7696 (mp) REVERT: C 60 PHE cc_start: 0.7679 (m-80) cc_final: 0.7286 (m-10) REVERT: C 70 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7339 (mmm160) REVERT: C 156 ASP cc_start: 0.7762 (t0) cc_final: 0.7504 (t0) REVERT: G 31 ASN cc_start: 0.8574 (t0) cc_final: 0.8293 (t0) REVERT: G 81 MET cc_start: 0.6450 (tmm) cc_final: 0.5748 (tmm) REVERT: G 82 ASP cc_start: 0.7410 (m-30) cc_final: 0.7180 (m-30) REVERT: G 93 VAL cc_start: 0.6787 (OUTLIER) cc_final: 0.6527 (p) REVERT: J 137 TYR cc_start: 0.8234 (t80) cc_final: 0.7708 (t80) REVERT: K 143 LYS cc_start: 0.8569 (pttp) cc_final: 0.7949 (pttm) REVERT: K 145 GLN cc_start: 0.8393 (mp10) cc_final: 0.8078 (pm20) REVERT: K 368 ASP cc_start: 0.8042 (t0) cc_final: 0.7708 (m-30) REVERT: M 142 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7782 (mtp-110) REVERT: P 28 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6877 (p) REVERT: Q 4 MET cc_start: 0.6946 (mtp) cc_final: 0.6590 (mtp) outliers start: 81 outliers final: 60 residues processed: 542 average time/residue: 0.4282 time to fit residues: 360.1980 Evaluate side-chains 553 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 490 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 520 THR Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 34 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 52 PHE Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 326 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN K 305 ASN L 267 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123463 restraints weight = 51789.562| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.53 r_work: 0.3546 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29421 Z= 0.191 Angle : 0.633 10.669 40022 Z= 0.324 Chirality : 0.044 0.239 4527 Planarity : 0.005 0.056 5105 Dihedral : 5.461 55.720 4268 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.63 % Allowed : 13.79 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3529 helix: 0.32 (0.17), residues: 828 sheet: 0.40 (0.18), residues: 851 loop : -0.21 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 106 HIS 0.006 0.001 HIS P 52 PHE 0.032 0.002 PHE F 122 TYR 0.029 0.002 TYR D 120 ARG 0.012 0.001 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 11) link_NAG-ASN : angle 3.01854 ( 33) hydrogen bonds : bond 0.04167 ( 1169) hydrogen bonds : angle 5.04679 ( 3069) SS BOND : bond 0.00517 ( 29) SS BOND : angle 1.66487 ( 58) covalent geometry : bond 0.00455 (29381) covalent geometry : angle 0.62411 (39931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 506 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7354 (t0) cc_final: 0.7106 (t0) REVERT: B 304 PHE cc_start: 0.8062 (t80) cc_final: 0.7615 (t80) REVERT: B 319 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7263 (ttt90) REVERT: B 368 ASP cc_start: 0.7109 (t0) cc_final: 0.6860 (t0) REVERT: B 401 ASP cc_start: 0.7301 (m-30) cc_final: 0.6955 (m-30) REVERT: B 554 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7568 (mp) REVERT: C 60 PHE cc_start: 0.7628 (m-80) cc_final: 0.7260 (m-10) REVERT: C 70 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7257 (mmm160) REVERT: C 160 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7211 (ttp80) REVERT: E 211 ASN cc_start: 0.7435 (m110) cc_final: 0.7214 (m-40) REVERT: G 31 ASN cc_start: 0.8536 (t0) cc_final: 0.8267 (t0) REVERT: G 36 TRP cc_start: 0.7499 (m100) cc_final: 0.7257 (m100) REVERT: G 81 MET cc_start: 0.6314 (tmm) cc_final: 0.5443 (tmm) REVERT: G 93 VAL cc_start: 0.6653 (OUTLIER) cc_final: 0.6444 (p) REVERT: J 137 TYR cc_start: 0.8128 (t80) cc_final: 0.7566 (t80) REVERT: K 368 ASP cc_start: 0.7709 (t0) cc_final: 0.7485 (m-30) REVERT: K 499 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: L 112 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8122 (mp) REVERT: M 142 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7571 (ttm-80) REVERT: N 147 PHE cc_start: 0.6524 (t80) cc_final: 0.5845 (m-80) REVERT: N 177 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5157 (mt-10) REVERT: O 122 PHE cc_start: 0.5970 (p90) cc_final: 0.5123 (p90) REVERT: P 28 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6876 (p) REVERT: Q 4 MET cc_start: 0.6791 (mtp) cc_final: 0.6395 (mtp) outliers start: 83 outliers final: 62 residues processed: 550 average time/residue: 0.4621 time to fit residues: 395.5130 Evaluate side-chains 564 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 496 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 145 GLN Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 499 GLU Chi-restraints excluded: chain K residue 520 THR Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 177 GLU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 39 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 203 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 314 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN K 145 GLN L 267 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125230 restraints weight = 51772.007| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.55 r_work: 0.3560 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29421 Z= 0.154 Angle : 0.613 10.783 40022 Z= 0.314 Chirality : 0.043 0.239 4527 Planarity : 0.005 0.055 5105 Dihedral : 5.360 55.700 4268 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.59 % Allowed : 13.92 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3529 helix: 0.46 (0.17), residues: 827 sheet: 0.45 (0.18), residues: 847 loop : -0.17 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 106 HIS 0.005 0.001 HIS M 38 PHE 0.034 0.002 PHE F 122 TYR 0.026 0.001 TYR D 120 ARG 0.013 0.000 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 2.75590 ( 33) hydrogen bonds : bond 0.03916 ( 1169) hydrogen bonds : angle 4.97423 ( 3069) SS BOND : bond 0.00423 ( 29) SS BOND : angle 1.59814 ( 58) covalent geometry : bond 0.00364 (29381) covalent geometry : angle 0.60578 (39931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 508 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7373 (t0) cc_final: 0.7120 (t0) REVERT: B 304 PHE cc_start: 0.8076 (t80) cc_final: 0.7593 (t80) REVERT: B 319 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7208 (ttt90) REVERT: B 368 ASP cc_start: 0.7130 (t0) cc_final: 0.6841 (t0) REVERT: B 401 ASP cc_start: 0.7269 (m-30) cc_final: 0.6932 (m-30) REVERT: B 554 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 60 PHE cc_start: 0.7664 (m-80) cc_final: 0.7272 (m-10) REVERT: C 70 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.7195 (mmm160) REVERT: C 160 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7209 (ttp80) REVERT: C 165 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8463 (p) REVERT: E 122 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7306 (mp) REVERT: G 31 ASN cc_start: 0.8496 (t0) cc_final: 0.8217 (t0) REVERT: G 36 TRP cc_start: 0.7466 (m100) cc_final: 0.7217 (m-10) REVERT: G 93 VAL cc_start: 0.6693 (OUTLIER) cc_final: 0.6462 (p) REVERT: J 73 SER cc_start: 0.8561 (p) cc_final: 0.8185 (m) REVERT: J 137 TYR cc_start: 0.8068 (t80) cc_final: 0.7451 (t80) REVERT: K 368 ASP cc_start: 0.7700 (t0) cc_final: 0.7422 (m-30) REVERT: K 499 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6620 (mm-30) REVERT: L 112 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8118 (mp) REVERT: L 239 ASP cc_start: 0.8587 (t0) cc_final: 0.8306 (t0) REVERT: M 142 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7650 (mtp-110) REVERT: N 151 MET cc_start: 0.7366 (mpp) cc_final: 0.6943 (mmm) REVERT: N 177 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5153 (mt-10) REVERT: P 19 LYS cc_start: 0.6739 (ttmt) cc_final: 0.6439 (ttmt) REVERT: P 28 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6831 (p) REVERT: Q 4 MET cc_start: 0.6699 (mtp) cc_final: 0.6238 (mtp) REVERT: R 121 GLN cc_start: 0.7553 (mm110) cc_final: 0.7258 (mm110) REVERT: S 106 MET cc_start: 0.7515 (ppp) cc_final: 0.7239 (ppp) outliers start: 82 outliers final: 60 residues processed: 551 average time/residue: 0.4328 time to fit residues: 370.7381 Evaluate side-chains 564 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 496 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 499 GLU Chi-restraints excluded: chain K residue 520 THR Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 177 GLU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 52 PHE Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 265 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN K 305 ASN L 267 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.150957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124704 restraints weight = 51557.962| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.56 r_work: 0.3555 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29421 Z= 0.170 Angle : 0.628 14.420 40022 Z= 0.321 Chirality : 0.044 0.239 4527 Planarity : 0.005 0.066 5105 Dihedral : 5.354 55.694 4268 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.40 % Allowed : 14.46 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3529 helix: 0.42 (0.17), residues: 830 sheet: 0.45 (0.18), residues: 848 loop : -0.20 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 106 HIS 0.005 0.001 HIS P 52 PHE 0.032 0.002 PHE O 122 TYR 0.026 0.002 TYR D 120 ARG 0.014 0.000 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 11) link_NAG-ASN : angle 2.59532 ( 33) hydrogen bonds : bond 0.04024 ( 1169) hydrogen bonds : angle 4.98905 ( 3069) SS BOND : bond 0.00487 ( 29) SS BOND : angle 1.65334 ( 58) covalent geometry : bond 0.00404 (29381) covalent geometry : angle 0.62073 (39931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 504 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7700 (t0) cc_final: 0.7440 (t0) REVERT: B 255 ARG cc_start: 0.8102 (mmt90) cc_final: 0.7842 (mpt-90) REVERT: B 304 PHE cc_start: 0.8362 (t80) cc_final: 0.7842 (t80) REVERT: B 319 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7382 (ttt90) REVERT: B 368 ASP cc_start: 0.7460 (t0) cc_final: 0.7142 (t0) REVERT: B 401 ASP cc_start: 0.7448 (m-30) cc_final: 0.7115 (m-30) REVERT: B 554 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 60 PHE cc_start: 0.7714 (m-80) cc_final: 0.7292 (m-10) REVERT: C 70 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7360 (mmm160) REVERT: C 160 ARG cc_start: 0.7663 (ttp80) cc_final: 0.7409 (ttp80) REVERT: C 165 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (p) REVERT: D 93 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7209 (mp) REVERT: E 122 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7452 (mp) REVERT: G 31 ASN cc_start: 0.8556 (t0) cc_final: 0.8276 (t0) REVERT: G 93 VAL cc_start: 0.6814 (OUTLIER) cc_final: 0.6532 (p) REVERT: J 73 SER cc_start: 0.8616 (p) cc_final: 0.8360 (m) REVERT: J 137 TYR cc_start: 0.8236 (t80) cc_final: 0.7639 (t80) REVERT: K 85 ASN cc_start: 0.7824 (p0) cc_final: 0.7087 (t0) REVERT: K 335 ARG cc_start: 0.8599 (ttt-90) cc_final: 0.8171 (ttt-90) REVERT: K 368 ASP cc_start: 0.8003 (t0) cc_final: 0.7640 (m-30) REVERT: K 499 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: L 112 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8228 (mp) REVERT: M 142 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7791 (mtp-110) REVERT: N 151 MET cc_start: 0.7528 (mpp) cc_final: 0.7055 (mmm) REVERT: N 177 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5619 (mt-10) REVERT: P 19 LYS cc_start: 0.6769 (ttmt) cc_final: 0.6292 (tppt) REVERT: P 28 THR cc_start: 0.7093 (OUTLIER) cc_final: 0.6879 (p) REVERT: Q 4 MET cc_start: 0.6858 (mtp) cc_final: 0.6396 (mtp) REVERT: R 121 GLN cc_start: 0.7658 (mm110) cc_final: 0.7340 (mm110) REVERT: S 106 MET cc_start: 0.7634 (ppp) cc_final: 0.7336 (ppp) outliers start: 76 outliers final: 60 residues processed: 545 average time/residue: 0.4174 time to fit residues: 353.6262 Evaluate side-chains 568 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 499 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 499 GLU Chi-restraints excluded: chain K residue 520 THR Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 177 GLU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 52 PHE Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 20 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 172 optimal weight: 0.0170 chunk 98 optimal weight: 1.9990 chunk 348 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 ASN L 267 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.150585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124580 restraints weight = 51583.860| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.52 r_work: 0.3566 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29421 Z= 0.152 Angle : 0.623 15.418 40022 Z= 0.319 Chirality : 0.043 0.239 4527 Planarity : 0.005 0.070 5105 Dihedral : 5.304 55.699 4268 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.25 % Allowed : 15.00 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3529 helix: 0.50 (0.17), residues: 830 sheet: 0.44 (0.17), residues: 858 loop : -0.18 (0.15), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 134 HIS 0.005 0.001 HIS P 35 PHE 0.033 0.002 PHE F 122 TYR 0.026 0.001 TYR D 120 ARG 0.014 0.000 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 11) link_NAG-ASN : angle 2.45232 ( 33) hydrogen bonds : bond 0.03884 ( 1169) hydrogen bonds : angle 4.94984 ( 3069) SS BOND : bond 0.00440 ( 29) SS BOND : angle 1.64177 ( 58) covalent geometry : bond 0.00361 (29381) covalent geometry : angle 0.61693 (39931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7058 Ramachandran restraints generated. 3529 Oldfield, 0 Emsley, 3529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 502 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ASN cc_start: 0.7662 (t0) cc_final: 0.7382 (t0) REVERT: B 255 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7858 (mpt-90) REVERT: B 304 PHE cc_start: 0.8351 (t80) cc_final: 0.7842 (t80) REVERT: B 319 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7382 (ttt90) REVERT: B 368 ASP cc_start: 0.7426 (t0) cc_final: 0.7109 (t0) REVERT: B 401 ASP cc_start: 0.7397 (m-30) cc_final: 0.7093 (m-30) REVERT: B 554 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7599 (mp) REVERT: C 60 PHE cc_start: 0.7741 (m-80) cc_final: 0.7317 (m-10) REVERT: C 70 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7381 (mmm160) REVERT: C 160 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7414 (ttp80) REVERT: C 165 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (p) REVERT: D 93 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7231 (mp) REVERT: E 122 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7497 (mp) REVERT: G 31 ASN cc_start: 0.8554 (t0) cc_final: 0.8283 (t0) REVERT: G 93 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6511 (p) REVERT: J 73 SER cc_start: 0.8589 (p) cc_final: 0.8344 (m) REVERT: J 137 TYR cc_start: 0.8236 (t80) cc_final: 0.7651 (t80) REVERT: K 85 ASN cc_start: 0.7837 (p0) cc_final: 0.7113 (t0) REVERT: K 368 ASP cc_start: 0.7989 (t0) cc_final: 0.7642 (m-30) REVERT: K 499 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: L 112 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8170 (mp) REVERT: M 142 ARG cc_start: 0.8078 (ttm110) cc_final: 0.7793 (mtp-110) REVERT: N 151 MET cc_start: 0.7547 (mpp) cc_final: 0.7066 (mmm) REVERT: N 177 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5388 (mt-10) REVERT: Q 4 MET cc_start: 0.6930 (mtp) cc_final: 0.6429 (mtp) REVERT: R 121 GLN cc_start: 0.7665 (mm110) cc_final: 0.7355 (mm110) REVERT: S 106 MET cc_start: 0.7603 (ppp) cc_final: 0.7305 (ppp) outliers start: 71 outliers final: 55 residues processed: 541 average time/residue: 0.4188 time to fit residues: 351.6746 Evaluate side-chains 557 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 494 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 171 MET Chi-restraints excluded: chain E residue 206 PHE Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain K residue 120 GLN Chi-restraints excluded: chain K residue 255 ARG Chi-restraints excluded: chain K residue 281 VAL Chi-restraints excluded: chain K residue 307 LEU Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 499 GLU Chi-restraints excluded: chain K residue 520 THR Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain N residue 55 PHE Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 177 GLU Chi-restraints excluded: chain N residue 206 PHE Chi-restraints excluded: chain O residue 120 LEU Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 52 PHE Chi-restraints excluded: chain S residue 77 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 200 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 285 optimal weight: 0.3980 chunk 180 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 316 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 141 GLN L 267 HIS N 123 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124971 restraints weight = 51635.634| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.51 r_work: 0.3567 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29421 Z= 0.155 Angle : 0.622 15.083 40022 Z= 0.318 Chirality : 0.043 0.239 4527 Planarity : 0.005 0.060 5105 Dihedral : 5.267 55.691 4268 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.25 % Allowed : 15.25 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3529 helix: 0.58 (0.17), residues: 822 sheet: 0.43 (0.17), residues: 870 loop : -0.18 (0.15), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 112 HIS 0.006 0.001 HIS P 35 PHE 0.033 0.002 PHE O 122 TYR 0.025 0.001 TYR D 120 ARG 0.014 0.000 ARG N 76 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 11) link_NAG-ASN : angle 2.39259 ( 33) hydrogen bonds : bond 0.03885 ( 1169) hydrogen bonds : angle 4.93339 ( 3069) SS BOND : bond 0.00457 ( 29) SS BOND : angle 1.60346 ( 58) covalent geometry : bond 0.00369 (29381) covalent geometry : angle 0.61571 (39931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21791.65 seconds wall clock time: 385 minutes 39.06 seconds (23139.06 seconds total)