Starting phenix.real_space_refine on Thu Mar 5 01:03:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cec_30342/03_2026/7cec_30342.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Mn 3 7.51 5 S 93 5.16 5 C 11061 2.51 5 N 2996 2.21 5 O 3404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17561 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4308 Classifications: {'peptide': 553} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 521} Chain breaks: 6 Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3320 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Chain breaks: 2 Chain: "C" Number of atoms: 4421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 33, 'TRANS': 540} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 574, 4412 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 33, 'TRANS': 540} Chain breaks: 2 bond proxies already assigned to first conformer: 4498 Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "E" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 357 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "F" Number of atoms: 1360 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Conformer: "B" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} bond proxies already assigned to first conformer: 1375 Chain: "G" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1252 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 954 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1080 Classifications: {'peptide': 140} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 129} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' MN': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1 residue: pdb=" N AGLN C2767 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C2767 " occ=0.50 Time building chain proxies: 5.12, per 1000 atoms: 0.29 Number of scatterers: 17561 At special positions: 0 Unit cell: (145.803, 192.549, 149.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 Ca 4 19.99 S 93 16.00 O 3404 8.00 N 2996 7.00 C 11061 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 71 " distance=2.06 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 131 " distance=2.04 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 539 " distance=2.02 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.01 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=2.02 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.04 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C2723 " - pdb=" SG CYS E1585 " distance=2.04 Simple disulfide: pdb=" SG CYS C2899 " - pdb=" SG CYS C2929 " distance=2.04 Simple disulfide: pdb=" SG CYS C3090 " - pdb=" SG CYS C3115 " distance=2.02 Simple disulfide: pdb=" SG CYS C3261 " - pdb=" SG CYS C3292 " distance=2.04 Simple disulfide: pdb=" SG CYS D1785 " - pdb=" SG CYS E1600 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 112 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 112 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " 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 BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1004 " - " ASN A 261 " " NAG A1005 " - " ASN A 347 " " NAG B1004 " - " ASN B 249 " " NAG B1005 " - " ASN B 343 " " NAG B1006 " - " ASN B 386 " " NAG C3402 " - " ASN C3257 " " NAG J 1 " - " ASN C3287 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 920.4 milliseconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 35 sheets defined 19.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 161 through 165 removed outlier: 4.469A pdb=" N SER A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.515A pdb=" N TRP A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.513A pdb=" N HIS A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 14 through 20 removed outlier: 3.558A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.921A pdb=" N SER B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.671A pdb=" N GLN B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.300A pdb=" N GLY B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.917A pdb=" N HIS B 292 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.836A pdb=" N LYS B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.712A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'C' and resid 2706 through 2732 removed outlier: 3.707A pdb=" N LEU C2710 " --> pdb=" O HIS C2706 " (cutoff:3.500A) Processing helix chain 'C' and resid 2754 through 2758 removed outlier: 3.712A pdb=" N ALA C2757 " --> pdb=" O ALA C2754 " (cutoff:3.500A) Processing helix chain 'C' and resid 2870 through 2874 removed outlier: 4.035A pdb=" N PHE C2874 " --> pdb=" O PRO C2871 " (cutoff:3.500A) Processing helix chain 'C' and resid 2937 through 2942 Processing helix chain 'C' and resid 3056 through 3060 Processing helix chain 'C' and resid 3074 through 3081 removed outlier: 3.595A pdb=" N ARG C3079 " --> pdb=" O PRO C3075 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU C3080 " --> pdb=" O SER C3076 " (cutoff:3.500A) Processing helix chain 'C' and resid 3117 through 3121 removed outlier: 3.619A pdb=" N VAL C3121 " --> pdb=" O ASP C3118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1741 through 1785 Processing helix chain 'E' and resid 1567 through 1596 removed outlier: 3.805A pdb=" N TYR E1575 " --> pdb=" O ALA E1571 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E1588 " --> pdb=" O LYS E1584 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E1590 " --> pdb=" O ILE E1586 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP E1591 " --> pdb=" O ARG E1587 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.815A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.000A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 122 removed outlier: 3.620A pdb=" N LEU F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 164 removed outlier: 3.742A pdb=" N ASP F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Proline residue: F 156 - end of helix removed outlier: 3.570A pdb=" N LYS F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.633A pdb=" N ASP G 82 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 119 through 159 removed outlier: 4.081A pdb=" N LEU G 130 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Proline residue: G 132 - end of helix Proline residue: G 151 - end of helix Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 124 through 156 Proline residue: I 132 - end of helix Proline residue: I 151 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 14 removed outlier: 5.169A pdb=" N SER A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 417 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA A 428 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY A 415 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLY A 430 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE A 413 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 30 removed outlier: 3.879A pdb=" N SER A 24 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 39 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 62 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR A 72 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 113 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 173 removed outlier: 3.650A pdb=" N ILE A 180 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 removed outlier: 4.384A pdb=" N HIS A 282 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS A 270 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.709A pdb=" N GLN A 316 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY A 325 " --> pdb=" O GLN A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 371 through 376 removed outlier: 3.675A pdb=" N ILE A 386 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 400 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 446 through 447 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.670A pdb=" N VAL A 476 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 525 through 531 removed outlier: 3.591A pdb=" N ALA A 592 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.200A pdb=" N GLN B 98 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 94 through 95 removed outlier: 4.015A pdb=" N ILE B 408 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 111 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 206 removed outlier: 6.239A pdb=" N VAL B 202 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N SER B 166 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER B 204 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 164 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR B 127 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 165 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 254 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 336 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 2737 through 2740 removed outlier: 7.195A pdb=" N LYS C2763 " --> pdb=" O ASP C2903 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C2905 " --> pdb=" O ALA C2761 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C2761 " --> pdb=" O LEU C2905 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 2816 through 2819 removed outlier: 3.777A pdb=" N MET C2795 " --> pdb=" O MET C2785 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C2799 " --> pdb=" O PHE C2781 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE C2781 " --> pdb=" O LEU C2799 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE C2876 " --> pdb=" O LEU C2747 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C2746 " --> pdb=" O GLU C2916 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 2954 through 2955 Processing sheet with id=AC1, first strand: chain 'C' and resid 3046 through 3052 removed outlier: 6.418A pdb=" N VAL C3041 " --> pdb=" O VAL C3048 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER C3050 " --> pdb=" O VAL C3039 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C3039 " --> pdb=" O SER C3050 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C3042 " --> pdb=" O GLN C3028 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 2978 through 2980 removed outlier: 6.446A pdb=" N LEU C2991 " --> pdb=" O LEU C2979 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 2978 through 2980 removed outlier: 6.446A pdb=" N LEU C2991 " --> pdb=" O LEU C2979 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 3095 through 3096 Processing sheet with id=AC5, first strand: chain 'C' and resid 3220 through 3223 removed outlier: 7.256A pdb=" N LEU C3215 " --> pdb=" O GLN C3222 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C3152 " --> pdb=" O ASN C3264 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C3264 " --> pdb=" O GLY C3152 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N HIS C3154 " --> pdb=" O ILE C3262 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE C3262 " --> pdb=" O HIS C3154 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE C3258 " --> pdb=" O GLY C3129 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 3134 through 3136 removed outlier: 5.083A pdb=" N ARG C3243 " --> pdb=" O ALA C3166 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA C3166 " --> pdb=" O ARG C3243 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU C3161 " --> pdb=" O LEU C3176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C3176 " --> pdb=" O LEU C3161 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.186A pdb=" N THR F 33 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET F 34 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.730A pdb=" N HIS F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.978A pdb=" N MET G 11 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.517A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 34 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N HIS H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.553A pdb=" N ALA I 13 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLN I 37 " --> pdb=" O PRO I 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 19 through 24 663 hydrogen bonds defined for protein. 1731 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: 4.17 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3694 1.32 - 1.45: 4737 1.45 - 1.58: 9341 1.58 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 17908 Sorted by residual: bond pdb=" C ASP B 138 " pdb=" O ASP B 138 " ideal model delta sigma weight residual 1.237 1.195 0.042 1.17e-02 7.31e+03 1.26e+01 bond pdb=" CA ALA B 342 " pdb=" C ALA B 342 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.15e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.244 1.211 0.033 1.00e-02 1.00e+04 1.08e+01 bond pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 1.502 1.427 0.075 2.30e-02 1.89e+03 1.07e+01 bond pdb=" CA PRO A 425 " pdb=" C PRO A 425 " ideal model delta sigma weight residual 1.522 1.560 -0.039 1.19e-02 7.06e+03 1.06e+01 ... (remaining 17903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 23510 2.93 - 5.86: 628 5.86 - 8.79: 69 8.79 - 11.72: 19 11.72 - 14.65: 4 Bond angle restraints: 24230 Sorted by residual: angle pdb=" C TYR A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta sigma weight residual 119.83 109.15 10.68 1.08e+00 8.57e-01 9.78e+01 angle pdb=" N PRO A 425 " pdb=" CA PRO A 425 " pdb=" C PRO A 425 " ideal model delta sigma weight residual 111.03 121.46 -10.43 1.54e+00 4.22e-01 4.59e+01 angle pdb=" C THR C2836 " pdb=" N LEU C2837 " pdb=" CA LEU C2837 " ideal model delta sigma weight residual 120.38 128.70 -8.32 1.37e+00 5.33e-01 3.69e+01 angle pdb=" N ASP B 137 " pdb=" CA ASP B 137 " pdb=" C ASP B 137 " ideal model delta sigma weight residual 111.07 105.06 6.01 1.07e+00 8.73e-01 3.15e+01 angle pdb=" CA ALA B 342 " pdb=" C ALA B 342 " pdb=" N ASN B 343 " ideal model delta sigma weight residual 116.84 126.29 -9.45 1.71e+00 3.42e-01 3.06e+01 ... (remaining 24225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 9664 18.07 - 36.13: 1093 36.13 - 54.20: 154 54.20 - 72.27: 47 72.27 - 90.34: 16 Dihedral angle restraints: 10974 sinusoidal: 4551 harmonic: 6423 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -176.34 90.34 1 1.00e+01 1.00e-02 9.66e+01 dihedral pdb=" CB CYS B 28 " pdb=" SG CYS B 28 " pdb=" SG CYS B 55 " pdb=" CB CYS B 55 " ideal model delta sinusoidal sigma weight residual 93.00 179.97 -86.97 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS B 7 " pdb=" SG CYS B 7 " pdb=" SG CYS B 25 " pdb=" CB CYS B 25 " ideal model delta sinusoidal sigma weight residual 93.00 179.57 -86.57 1 1.00e+01 1.00e-02 9.03e+01 ... (remaining 10971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 2674 0.260 - 0.521: 14 0.521 - 0.781: 0 0.781 - 1.042: 0 1.042 - 1.302: 1 Chirality restraints: 2689 Sorted by residual: chirality pdb=" C1 NAG A1005 " pdb=" ND2 ASN A 347 " pdb=" C2 NAG A1005 " pdb=" O5 NAG A1005 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.24e+01 chirality pdb=" C2 NAG B1005 " pdb=" C1 NAG B1005 " pdb=" C3 NAG B1005 " pdb=" N2 NAG B1005 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C3287 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2686 not shown) Planarity restraints: 3147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D1762 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C ALA D1762 " 0.083 2.00e-02 2.50e+03 pdb=" O ALA D1762 " -0.031 2.00e-02 2.50e+03 pdb=" N ARG D1763 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 134 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C MET G 134 " 0.063 2.00e-02 2.50e+03 pdb=" O MET G 134 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU G 135 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D1758 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ALA D1758 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA D1758 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN D1759 " -0.021 2.00e-02 2.50e+03 ... (remaining 3144 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 350 2.55 - 3.14: 13920 3.14 - 3.73: 30065 3.73 - 4.31: 40684 4.31 - 4.90: 64919 Nonbonded interactions: 149938 Sorted by model distance: nonbonded pdb=" OE1 GLU B 169 " pdb="MN MN B1001 " model vdw 1.965 2.320 nonbonded pdb=" OD1 ASP B 226 " pdb="MN MN B1001 " model vdw 1.970 2.320 nonbonded pdb=" OE2 GLU B 229 " pdb="MN MN B1002 " model vdw 1.972 2.320 nonbonded pdb=" OD1 ASP A 301 " pdb=" OD1 ASP A 305 " model vdw 2.014 3.040 nonbonded pdb=" OD1 ASP A 363 " pdb=" OD1 ASP A 367 " model vdw 2.027 3.040 ... (remaining 149933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.960 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.011 0.106 17940 Z= 0.511 Angle : 1.206 21.933 24302 Z= 0.656 Chirality : 0.071 1.302 2689 Planarity : 0.008 0.067 3140 Dihedral : 15.059 89.094 6798 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 1.15 % Allowed : 10.52 % Favored : 88.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.15), residues: 2202 helix: -2.78 (0.20), residues: 353 sheet: -2.37 (0.18), residues: 661 loop : -2.46 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 154 TYR 0.027 0.003 TYR C3163 PHE 0.036 0.004 PHE H 79 TRP 0.025 0.004 TRP A 545 HIS 0.012 0.003 HIS A 28 Details of bonding type rmsd covalent geometry : bond 0.01067 (17908) covalent geometry : angle 1.17966 (24230) SS BOND : bond 0.00924 ( 24) SS BOND : angle 2.26543 ( 48) hydrogen bonds : bond 0.16546 ( 643) hydrogen bonds : angle 9.24757 ( 1731) link_BETA1-4 : bond 0.02268 ( 1) link_BETA1-4 : angle 3.05616 ( 3) link_NAG-ASN : bond 0.01140 ( 7) link_NAG-ASN : angle 8.05883 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.664 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 137 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 175 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 290 MET cc_start: 0.8963 (mmm) cc_final: 0.8728 (mmp) REVERT: C 3125 MET cc_start: 0.8906 (mmt) cc_final: 0.8697 (mmm) REVERT: E 1587 ARG cc_start: 0.9130 (mtt180) cc_final: 0.8874 (ptp-110) REVERT: I 133 MET cc_start: 0.8380 (tpt) cc_final: 0.7283 (ptt) outliers start: 22 outliers final: 10 residues processed: 128 average time/residue: 0.1610 time to fit residues: 30.6918 Evaluate side-chains 77 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 2868 ASN Chi-restraints excluded: chain G residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 232 ASN A 277 HIS A 308 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 485 ASN A 534 GLN B 30 ASN B 109 GLN B 282 HIS B 292 HIS B 309 ASN ** C2706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2725 GLN C2805 HIS C2959 GLN C2994 GLN C3128 HIS C3220 GLN ** C3280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1588 ASN E1602 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 105 GLN A F 105 GLN B G 6 GLN H 76 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.038495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.028493 restraints weight = 285151.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.029754 restraints weight = 123937.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.030600 restraints weight = 71849.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031167 restraints weight = 49153.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031548 restraints weight = 37598.388| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17940 Z= 0.206 Angle : 0.734 14.766 24302 Z= 0.376 Chirality : 0.048 0.716 2689 Planarity : 0.005 0.049 3140 Dihedral : 7.156 59.277 2624 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.67 % Allowed : 13.54 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.16), residues: 2202 helix: -1.54 (0.24), residues: 360 sheet: -1.98 (0.19), residues: 617 loop : -2.16 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 71 TYR 0.016 0.002 TYR F 58 PHE 0.015 0.002 PHE A 354 TRP 0.015 0.002 TRP H 36 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00421 (17908) covalent geometry : angle 0.71799 (24230) SS BOND : bond 0.00401 ( 24) SS BOND : angle 1.24334 ( 48) hydrogen bonds : bond 0.05402 ( 643) hydrogen bonds : angle 7.54206 ( 1731) link_BETA1-4 : bond 0.00034 ( 1) link_BETA1-4 : angle 1.92519 ( 3) link_NAG-ASN : bond 0.00787 ( 7) link_NAG-ASN : angle 4.95910 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7932 (ptt) REVERT: B 173 MET cc_start: 0.8834 (tpp) cc_final: 0.8585 (mmm) REVERT: C 2783 MET cc_start: 0.9069 (ppp) cc_final: 0.8868 (ppp) REVERT: C 2795 MET cc_start: 0.8639 (tmm) cc_final: 0.8199 (tmm) REVERT: C 2902 MET cc_start: 0.7966 (tpp) cc_final: 0.7620 (mmt) REVERT: E 1583 MET cc_start: 0.9026 (mmm) cc_final: 0.8784 (mmp) REVERT: E 1587 ARG cc_start: 0.9178 (mtt180) cc_final: 0.8908 (ptp-110) REVERT: G 103 LYS cc_start: 0.9145 (tttm) cc_final: 0.8828 (tttp) REVERT: G 154 ASP cc_start: 0.9209 (m-30) cc_final: 0.8946 (t0) REVERT: H 0 MET cc_start: 0.8295 (ppp) cc_final: 0.8092 (ppp) REVERT: I 21 MET cc_start: 0.9022 (mpp) cc_final: 0.8355 (tmm) outliers start: 30 outliers final: 12 residues processed: 110 average time/residue: 0.1264 time to fit residues: 22.3289 Evaluate side-chains 80 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 106 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 195 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.038214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.027927 restraints weight = 347108.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.029263 restraints weight = 137452.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.030155 restraints weight = 76725.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.030751 restraints weight = 51329.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.031157 restraints weight = 38726.279| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17940 Z= 0.223 Angle : 0.720 14.052 24302 Z= 0.365 Chirality : 0.047 0.668 2689 Planarity : 0.004 0.042 3140 Dihedral : 6.728 58.800 2610 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.93 % Allowed : 15.89 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.16), residues: 2202 helix: -0.84 (0.25), residues: 360 sheet: -1.89 (0.19), residues: 624 loop : -2.03 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1577 TYR 0.015 0.001 TYR F 58 PHE 0.018 0.002 PHE A 354 TRP 0.015 0.002 TRP F 47 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00467 (17908) covalent geometry : angle 0.70419 (24230) SS BOND : bond 0.00592 ( 24) SS BOND : angle 1.54797 ( 48) hydrogen bonds : bond 0.05033 ( 643) hydrogen bonds : angle 7.13958 ( 1731) link_BETA1-4 : bond 0.00060 ( 1) link_BETA1-4 : angle 1.96711 ( 3) link_NAG-ASN : bond 0.00780 ( 7) link_NAG-ASN : angle 4.73544 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8117 (ptt) cc_final: 0.7893 (ptt) REVERT: B 173 MET cc_start: 0.8776 (tpp) cc_final: 0.8562 (mmm) REVERT: C 2783 MET cc_start: 0.9150 (ppp) cc_final: 0.8930 (ppp) REVERT: C 2785 MET cc_start: 0.9182 (ptm) cc_final: 0.8461 (ptm) REVERT: C 2795 MET cc_start: 0.8655 (tmm) cc_final: 0.7309 (tmm) REVERT: C 2902 MET cc_start: 0.8024 (tpp) cc_final: 0.7620 (mmt) REVERT: C 3224 MET cc_start: 0.7246 (tpt) cc_final: 0.6705 (tpt) REVERT: E 1583 MET cc_start: 0.9077 (mmm) cc_final: 0.8780 (mmm) REVERT: E 1587 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8933 (ptp-110) REVERT: G 141 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8925 (mm) REVERT: I 21 MET cc_start: 0.9078 (mpp) cc_final: 0.8504 (tmm) outliers start: 35 outliers final: 23 residues processed: 101 average time/residue: 0.1226 time to fit residues: 20.4155 Evaluate side-chains 88 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 212 optimal weight: 0.0570 chunk 88 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C2706 HIS C3280 GLN F 39 GLN F 141 GLN ** H 77 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 = 0.3505 r_free = 0.3505 target = 0.038957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.028609 restraints weight = 349978.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.030008 restraints weight = 135355.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.030928 restraints weight = 74528.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.031545 restraints weight = 49574.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.031955 restraints weight = 37114.947| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17940 Z= 0.154 Angle : 0.641 12.364 24302 Z= 0.324 Chirality : 0.046 0.576 2689 Planarity : 0.004 0.044 3140 Dihedral : 6.263 58.161 2608 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.93 % Allowed : 16.15 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2202 helix: -0.29 (0.26), residues: 359 sheet: -1.74 (0.19), residues: 625 loop : -1.87 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 94 TYR 0.017 0.001 TYR G 36 PHE 0.014 0.001 PHE A 354 TRP 0.015 0.002 TRP A 29 HIS 0.006 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00325 (17908) covalent geometry : angle 0.62792 (24230) SS BOND : bond 0.00395 ( 24) SS BOND : angle 1.30810 ( 48) hydrogen bonds : bond 0.04202 ( 643) hydrogen bonds : angle 6.61433 ( 1731) link_BETA1-4 : bond 0.00211 ( 1) link_BETA1-4 : angle 1.53694 ( 3) link_NAG-ASN : bond 0.00742 ( 7) link_NAG-ASN : angle 4.10084 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.618 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: A 144 MET cc_start: 0.3936 (mtt) cc_final: 0.3660 (mtt) REVERT: A 540 MET cc_start: 0.8157 (ptt) cc_final: 0.7907 (ptt) REVERT: C 2783 MET cc_start: 0.9217 (ppp) cc_final: 0.9002 (ppp) REVERT: C 2785 MET cc_start: 0.9163 (ptm) cc_final: 0.8418 (ptm) REVERT: C 2795 MET cc_start: 0.8712 (tmm) cc_final: 0.7496 (tmm) REVERT: C 2842 MET cc_start: 0.8867 (ttm) cc_final: 0.8365 (ttp) REVERT: C 2902 MET cc_start: 0.7907 (tpp) cc_final: 0.7437 (mmt) REVERT: C 3224 MET cc_start: 0.7052 (tpt) cc_final: 0.6400 (tpt) REVERT: E 1573 MET cc_start: 0.9687 (tpp) cc_final: 0.9428 (tmm) REVERT: E 1574 ASP cc_start: 0.9133 (p0) cc_final: 0.8839 (p0) REVERT: E 1577 ARG cc_start: 0.9509 (mtm110) cc_final: 0.9238 (mtm110) REVERT: E 1583 MET cc_start: 0.9125 (mmm) cc_final: 0.8787 (mmm) REVERT: E 1587 ARG cc_start: 0.9195 (mtt180) cc_final: 0.8969 (ptp-110) REVERT: I 21 MET cc_start: 0.9064 (mpp) cc_final: 0.8595 (tmm) outliers start: 35 outliers final: 24 residues processed: 111 average time/residue: 0.1289 time to fit residues: 23.1806 Evaluate side-chains 92 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3127 PHE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 96 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN C3015 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.038169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.027883 restraints weight = 350710.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.029213 restraints weight = 139184.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.030092 restraints weight = 77988.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.030667 restraints weight = 52286.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031079 restraints weight = 39679.508| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17940 Z= 0.224 Angle : 0.695 12.687 24302 Z= 0.347 Chirality : 0.046 0.567 2689 Planarity : 0.004 0.043 3140 Dihedral : 6.296 58.679 2608 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.34 % Allowed : 16.93 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.17), residues: 2202 helix: 0.04 (0.26), residues: 361 sheet: -1.79 (0.19), residues: 613 loop : -1.85 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 147 TYR 0.013 0.002 TYR C3163 PHE 0.019 0.002 PHE A 354 TRP 0.013 0.002 TRP C2939 HIS 0.008 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00470 (17908) covalent geometry : angle 0.68290 (24230) SS BOND : bond 0.00388 ( 24) SS BOND : angle 1.21476 ( 48) hydrogen bonds : bond 0.04463 ( 643) hydrogen bonds : angle 6.47789 ( 1731) link_BETA1-4 : bond 0.00080 ( 1) link_BETA1-4 : angle 1.73975 ( 3) link_NAG-ASN : bond 0.00681 ( 7) link_NAG-ASN : angle 4.09254 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.711 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: A 144 MET cc_start: 0.4272 (mtt) cc_final: 0.3971 (mtt) REVERT: A 540 MET cc_start: 0.8137 (ptt) cc_final: 0.7903 (ptt) REVERT: C 2820 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7344 (mm) REVERT: C 2902 MET cc_start: 0.8114 (tpp) cc_final: 0.7604 (mmt) REVERT: C 2984 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: C 3224 MET cc_start: 0.7238 (tpt) cc_final: 0.6470 (tpt) REVERT: E 1573 MET cc_start: 0.9707 (tpp) cc_final: 0.9460 (tmm) REVERT: E 1574 ASP cc_start: 0.9149 (p0) cc_final: 0.8852 (p0) REVERT: E 1577 ARG cc_start: 0.9547 (mtm110) cc_final: 0.9269 (mtm110) REVERT: E 1583 MET cc_start: 0.9148 (mmm) cc_final: 0.8876 (mmm) REVERT: I 21 MET cc_start: 0.9054 (mpp) cc_final: 0.8650 (tmm) REVERT: I 134 MET cc_start: 0.8044 (ptt) cc_final: 0.7371 (mtt) outliers start: 43 outliers final: 33 residues processed: 106 average time/residue: 0.1237 time to fit residues: 21.5153 Evaluate side-chains 98 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3116 THR Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 140 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 136 optimal weight: 0.0670 chunk 219 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN D1777 GLN ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.039222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.028685 restraints weight = 397154.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.030156 restraints weight = 144848.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031131 restraints weight = 78062.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.031776 restraints weight = 50919.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.032205 restraints weight = 37847.031| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17940 Z= 0.118 Angle : 0.632 14.062 24302 Z= 0.313 Chirality : 0.046 0.514 2689 Planarity : 0.003 0.043 3140 Dihedral : 5.933 57.964 2608 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.93 % Allowed : 17.29 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.17), residues: 2202 helix: 0.37 (0.27), residues: 361 sheet: -1.56 (0.20), residues: 621 loop : -1.68 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.014 0.001 TYR C3063 PHE 0.010 0.001 PHE A 354 TRP 0.014 0.001 TRP F 103 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00254 (17908) covalent geometry : angle 0.62256 (24230) SS BOND : bond 0.00339 ( 24) SS BOND : angle 0.95733 ( 48) hydrogen bonds : bond 0.03810 ( 643) hydrogen bonds : angle 6.19485 ( 1731) link_BETA1-4 : bond 0.00200 ( 1) link_BETA1-4 : angle 1.43376 ( 3) link_NAG-ASN : bond 0.00722 ( 7) link_NAG-ASN : angle 3.62688 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4178 (mtt) cc_final: 0.3930 (mtt) REVERT: A 540 MET cc_start: 0.8113 (ptt) cc_final: 0.7860 (ptt) REVERT: B 229 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8069 (mm-30) REVERT: C 2783 MET cc_start: 0.9268 (ppp) cc_final: 0.8648 (ppp) REVERT: C 2795 MET cc_start: 0.8331 (tmm) cc_final: 0.7597 (tmm) REVERT: C 2820 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7296 (mm) REVERT: C 2902 MET cc_start: 0.7962 (tpp) cc_final: 0.7495 (mmt) REVERT: C 3224 MET cc_start: 0.7200 (tpt) cc_final: 0.6498 (tpt) REVERT: E 1573 MET cc_start: 0.9728 (tpp) cc_final: 0.9496 (tmm) REVERT: E 1574 ASP cc_start: 0.9122 (p0) cc_final: 0.8796 (p0) REVERT: E 1577 ARG cc_start: 0.9531 (mtm110) cc_final: 0.9229 (mtm110) REVERT: E 1583 MET cc_start: 0.9169 (mmm) cc_final: 0.8867 (mmp) REVERT: F 82 MET cc_start: 0.8286 (ttm) cc_final: 0.8084 (ttm) REVERT: F 138 MET cc_start: 0.9070 (tpt) cc_final: 0.8824 (tpt) REVERT: G 103 LYS cc_start: 0.9142 (tttm) cc_final: 0.8776 (tttp) REVERT: I 21 MET cc_start: 0.8986 (mpp) cc_final: 0.8560 (tmm) outliers start: 35 outliers final: 27 residues processed: 108 average time/residue: 0.1228 time to fit residues: 21.2304 Evaluate side-chains 99 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 112 optimal weight: 0.0980 chunk 15 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 GLN A 547 GLN C2959 GLN D1777 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.037500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.027611 restraints weight = 288208.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.028785 restraints weight = 128491.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.029562 restraints weight = 75688.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.030069 restraints weight = 52652.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.030439 restraints weight = 40993.112| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 17940 Z= 0.350 Angle : 0.799 12.978 24302 Z= 0.397 Chirality : 0.049 0.620 2689 Planarity : 0.004 0.043 3140 Dihedral : 6.435 59.707 2608 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 2.60 % Allowed : 17.81 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.17), residues: 2202 helix: 0.29 (0.26), residues: 362 sheet: -1.82 (0.20), residues: 622 loop : -1.92 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 149 TYR 0.017 0.002 TYR F 79 PHE 0.024 0.002 PHE A 354 TRP 0.015 0.002 TRP C2939 HIS 0.007 0.002 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00731 (17908) covalent geometry : angle 0.78842 (24230) SS BOND : bond 0.00479 ( 24) SS BOND : angle 1.23691 ( 48) hydrogen bonds : bond 0.04858 ( 643) hydrogen bonds : angle 6.48861 ( 1731) link_BETA1-4 : bond 0.00105 ( 1) link_BETA1-4 : angle 2.25972 ( 3) link_NAG-ASN : bond 0.00602 ( 7) link_NAG-ASN : angle 4.17777 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 63 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4536 (mtt) cc_final: 0.4141 (mtt) REVERT: A 540 MET cc_start: 0.8081 (ptt) cc_final: 0.7824 (ptt) REVERT: C 2783 MET cc_start: 0.9254 (ppp) cc_final: 0.8582 (ppp) REVERT: C 2820 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7367 (mm) REVERT: C 2902 MET cc_start: 0.8232 (tpp) cc_final: 0.7679 (mmt) REVERT: C 3224 MET cc_start: 0.7455 (tpt) cc_final: 0.6942 (tpt) REVERT: E 1583 MET cc_start: 0.9129 (mmm) cc_final: 0.8824 (mmm) REVERT: F 82 MET cc_start: 0.8229 (ttm) cc_final: 0.7896 (ttt) REVERT: G 134 MET cc_start: 0.9104 (ttt) cc_final: 0.8818 (ttt) REVERT: I 21 MET cc_start: 0.9053 (mpp) cc_final: 0.8612 (tmm) REVERT: I 134 MET cc_start: 0.8135 (ptt) cc_final: 0.7479 (mtt) outliers start: 48 outliers final: 39 residues processed: 109 average time/residue: 0.1188 time to fit residues: 21.5285 Evaluate side-chains 97 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 57 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2984 GLN Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3116 THR Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3257 ASN Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1576 ASN Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 170 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN C2959 GLN D1777 GLN H 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.039070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.028453 restraints weight = 410090.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.029933 restraints weight = 148251.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.030903 restraints weight = 79600.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.031554 restraints weight = 52018.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.031987 restraints weight = 38634.662| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17940 Z= 0.124 Angle : 0.668 13.576 24302 Z= 0.329 Chirality : 0.046 0.526 2689 Planarity : 0.004 0.046 3140 Dihedral : 6.019 59.100 2608 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.82 % Allowed : 19.17 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2202 helix: 0.63 (0.27), residues: 357 sheet: -1.65 (0.20), residues: 630 loop : -1.60 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1577 TYR 0.015 0.001 TYR C3063 PHE 0.012 0.001 PHE C3127 TRP 0.017 0.002 TRP F 103 HIS 0.006 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00273 (17908) covalent geometry : angle 0.65744 (24230) SS BOND : bond 0.00418 ( 24) SS BOND : angle 1.53480 ( 48) hydrogen bonds : bond 0.03797 ( 643) hydrogen bonds : angle 6.13294 ( 1731) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 1.30691 ( 3) link_NAG-ASN : bond 0.00669 ( 7) link_NAG-ASN : angle 3.57241 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4344 (mtt) cc_final: 0.3939 (mtt) REVERT: A 540 MET cc_start: 0.8069 (ptt) cc_final: 0.7794 (ptt) REVERT: B 229 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: C 2783 MET cc_start: 0.9283 (ppp) cc_final: 0.8717 (ppp) REVERT: C 2820 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7273 (mm) REVERT: C 3224 MET cc_start: 0.7061 (tpt) cc_final: 0.6370 (tpt) REVERT: E 1573 MET cc_start: 0.9548 (tmm) cc_final: 0.8829 (tpt) REVERT: E 1574 ASP cc_start: 0.9347 (p0) cc_final: 0.8962 (p0) REVERT: E 1583 MET cc_start: 0.9127 (mmm) cc_final: 0.8821 (mmp) REVERT: G 78 MET cc_start: 0.8025 (tpt) cc_final: 0.7749 (tpp) REVERT: G 103 LYS cc_start: 0.9207 (tttm) cc_final: 0.8877 (tttp) REVERT: I 21 MET cc_start: 0.8975 (mpp) cc_final: 0.8664 (tmm) REVERT: I 134 MET cc_start: 0.8181 (ptt) cc_final: 0.7496 (mtt) outliers start: 33 outliers final: 28 residues processed: 102 average time/residue: 0.1248 time to fit residues: 21.0959 Evaluate side-chains 95 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3116 THR Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 2 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 190 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN C2959 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.037924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.027705 restraints weight = 340114.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.029000 restraints weight = 137698.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.029854 restraints weight = 78026.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.030415 restraints weight = 52802.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.030815 restraints weight = 40299.787| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17940 Z= 0.270 Angle : 0.770 16.761 24302 Z= 0.377 Chirality : 0.047 0.583 2689 Planarity : 0.004 0.109 3140 Dihedral : 6.224 59.426 2608 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.98 % Allowed : 19.06 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2202 helix: 0.44 (0.27), residues: 362 sheet: -1.80 (0.19), residues: 645 loop : -1.71 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1577 TYR 0.014 0.002 TYR F 79 PHE 0.023 0.002 PHE A 354 TRP 0.014 0.002 TRP C2939 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00571 (17908) covalent geometry : angle 0.75907 (24230) SS BOND : bond 0.00432 ( 24) SS BOND : angle 1.63287 ( 48) hydrogen bonds : bond 0.04328 ( 643) hydrogen bonds : angle 6.25171 ( 1731) link_BETA1-4 : bond 0.00102 ( 1) link_BETA1-4 : angle 1.89862 ( 3) link_NAG-ASN : bond 0.00636 ( 7) link_NAG-ASN : angle 3.84434 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4396 (mtt) cc_final: 0.3939 (mtt) REVERT: A 309 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: A 540 MET cc_start: 0.8117 (ptt) cc_final: 0.7879 (ptt) REVERT: C 2783 MET cc_start: 0.9312 (ppp) cc_final: 0.8647 (ppp) REVERT: C 2820 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7349 (mm) REVERT: C 3224 MET cc_start: 0.7398 (tpt) cc_final: 0.6932 (tpt) REVERT: E 1574 ASP cc_start: 0.9270 (p0) cc_final: 0.8971 (p0) REVERT: E 1583 MET cc_start: 0.9107 (mmm) cc_final: 0.8812 (mmp) REVERT: F 82 MET cc_start: 0.8173 (ttm) cc_final: 0.7971 (ttt) REVERT: I 21 MET cc_start: 0.9040 (mpp) cc_final: 0.8663 (tmm) REVERT: I 134 MET cc_start: 0.8385 (ptt) cc_final: 0.7774 (mtt) outliers start: 36 outliers final: 31 residues processed: 98 average time/residue: 0.1242 time to fit residues: 20.0924 Evaluate side-chains 91 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 58 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3116 THR Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 121 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 185 optimal weight: 0.0270 chunk 92 optimal weight: 8.9990 chunk 211 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.038532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.028367 restraints weight = 312531.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.029667 restraints weight = 129995.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.030531 restraints weight = 74136.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031106 restraints weight = 50241.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031493 restraints weight = 38287.944| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17940 Z= 0.169 Angle : 0.714 17.970 24302 Z= 0.349 Chirality : 0.046 0.551 2689 Planarity : 0.004 0.057 3140 Dihedral : 6.062 58.237 2608 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.93 % Allowed : 19.17 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2202 helix: 0.63 (0.27), residues: 361 sheet: -1.72 (0.20), residues: 635 loop : -1.63 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E1577 TYR 0.014 0.001 TYR C3063 PHE 0.016 0.001 PHE A 354 TRP 0.012 0.001 TRP A 190 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00363 (17908) covalent geometry : angle 0.70406 (24230) SS BOND : bond 0.00381 ( 24) SS BOND : angle 1.44842 ( 48) hydrogen bonds : bond 0.03925 ( 643) hydrogen bonds : angle 6.09916 ( 1731) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 1.63085 ( 3) link_NAG-ASN : bond 0.00633 ( 7) link_NAG-ASN : angle 3.58880 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.4559 (mtt) cc_final: 0.4094 (mtt) REVERT: A 540 MET cc_start: 0.8104 (ptt) cc_final: 0.7859 (ptt) REVERT: C 2783 MET cc_start: 0.9299 (ppp) cc_final: 0.8685 (ppp) REVERT: C 2820 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7315 (mm) REVERT: C 3125 MET cc_start: 0.8593 (mmm) cc_final: 0.8358 (tpt) REVERT: C 3224 MET cc_start: 0.7146 (tpt) cc_final: 0.6461 (tpt) REVERT: E 1583 MET cc_start: 0.9110 (mmm) cc_final: 0.8818 (mmp) REVERT: I 21 MET cc_start: 0.9006 (mpp) cc_final: 0.8563 (tmm) REVERT: I 133 MET cc_start: 0.4893 (mmm) cc_final: 0.4676 (mmt) REVERT: I 134 MET cc_start: 0.8314 (ptt) cc_final: 0.7779 (mtt) outliers start: 35 outliers final: 31 residues processed: 98 average time/residue: 0.1143 time to fit residues: 18.7554 Evaluate side-chains 96 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 3012 VAL Chi-restraints excluded: chain C residue 3116 THR Chi-restraints excluded: chain C residue 3121 VAL Chi-restraints excluded: chain C residue 3265 VAL Chi-restraints excluded: chain C residue 3271 LEU Chi-restraints excluded: chain E residue 1592 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 51 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 115 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.038082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.027871 restraints weight = 355486.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.029683 restraints weight = 145959.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.030406 restraints weight = 66980.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.030988 restraints weight = 42778.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.031097 restraints weight = 34720.395| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17940 Z= 0.225 Angle : 0.747 15.016 24302 Z= 0.366 Chirality : 0.046 0.568 2689 Planarity : 0.004 0.046 3140 Dihedral : 6.118 58.325 2608 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.98 % Allowed : 19.17 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 2202 helix: 0.62 (0.27), residues: 362 sheet: -1.72 (0.20), residues: 642 loop : -1.68 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E1577 TYR 0.013 0.001 TYR C3163 PHE 0.019 0.002 PHE A 354 TRP 0.012 0.002 TRP C2939 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00480 (17908) covalent geometry : angle 0.73680 (24230) SS BOND : bond 0.00413 ( 24) SS BOND : angle 1.46200 ( 48) hydrogen bonds : bond 0.04077 ( 643) hydrogen bonds : angle 6.15075 ( 1731) link_BETA1-4 : bond 0.00115 ( 1) link_BETA1-4 : angle 1.81714 ( 3) link_NAG-ASN : bond 0.00629 ( 7) link_NAG-ASN : angle 3.71890 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.21 seconds wall clock time: 85 minutes 14.54 seconds (5114.54 seconds total)