Starting phenix.real_space_refine on Sat Sep 12 19:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cec_30342/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cec_30342/09_2026/7cec_30342.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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: 4.82, per 1000 atoms: 0.27 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: 1.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.63 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: 4.21 Time building geometry restraints manager: 1.68 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: 9514 18.07 - 36.13: 1081 36.13 - 54.20: 151 54.20 - 72.27: 44 72.27 - 90.34: 16 Dihedral angle restraints: 10806 sinusoidal: 4383 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 10803 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.100 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 15.087 89.094 6630 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/Z covalent geometry : bond 0.01067 / 0.51 (17908) covalent geometry : angle 1.17966 / 0.65 (24230) SS BOND : bond 0.00924 / 0.52 ( 24) SS BOND : angle 2.26543 / 1.44 ( 48) hydrogen bonds : bond 0.16546 / 10.62 ( 643) hydrogen bonds : angle 9.24757 / 6.49 ( 1731) link_BETA1-4 : bond 0.02268 / 1.19 ( 1) link_BETA1-4 : angle 3.05616 / 2.50 ( 3) link_NAG-ASN : bond 0.01140 / 0.57 ( 7) link_NAG-ASN : angle 8.05883 / 6.00 ( 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 : 0.735 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: 0.1608 time to fit residues: 30.7625 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 : 0.864 ------------------------------------------------------------------------------- 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... 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 = 0.038516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.028524 restraints weight = 285261.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.029783 restraints weight = 123415.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.030627 restraints weight = 71651.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.031191 restraints weight = 49100.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.031565 restraints weight = 37645.389| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17940 Z= 0.205 Angle : 0.735 14.555 24302 Z= 0.376 Chirality : 0.048 0.697 2689 Planarity : 0.005 0.048 3140 Dihedral : 6.560 41.536 2456 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -1.53 (0.24), residues: 360 sheet: -1.96 (0.19), residues: 616 loop : -2.17 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C2742 TYR 0.016 0.002 TYR F 58 PHE 0.016 0.002 PHE A 354 TRP 0.016 0.002 TRP H 36 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (17908) covalent geometry : angle 0.71959 / 0.37 (24230) SS BOND : bond 0.00389 / 0.20 ( 24) SS BOND : angle 1.22402 / 0.78 ( 48) hydrogen bonds : bond 0.05327 / 3.47 ( 643) hydrogen bonds : angle 7.53288 / 5.27 ( 1731) link_BETA1-4 : bond 0.00670 / 0.35 ( 1) link_BETA1-4 : angle 1.88802 / 1.18 ( 3) link_NAG-ASN : bond 0.00794 / 0.39 ( 7) link_NAG-ASN : angle 4.88492 / 3.86 ( 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 113 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.738 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: 0.7928 (ptt) REVERT: B 173 MET cc_start: 0.8807 (tpp) cc_final: 0.8575 (mmm) REVERT: C 2783 MET cc_start: 0.9064 (ppp) cc_final: 0.8864 (ppp) REVERT: C 2795 MET cc_start: 0.8574 (tmm) cc_final: 0.8139 (tmm) REVERT: C 2902 MET cc_start: 0.7920 (tpp) cc_final: 0.7567 (mmt) REVERT: E 1583 MET cc_start: 0.9022 (mmm) cc_final: 0.8781 (mmp) REVERT: E 1587 ARG cc_start: 0.9168 (mtt180) cc_final: 0.8873 (ptp-110) REVERT: G 103 LYS cc_start: 0.9146 (tttm) cc_final: 0.8835 (tttp) REVERT: I 21 MET cc_start: 0.9019 (mpp) cc_final: 0.8351 (tmm) outliers start: 30 outliers final: 13 residues processed: 109 average time/residue: 0.1324 time to fit residues: 23.1783 Evaluate side-chains 81 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 206 THR 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: 7.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C3015 GLN F 39 GLN F 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.038079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.027864 restraints weight = 342363.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.029184 restraints weight = 137844.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.030058 restraints weight = 77357.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.030642 restraints weight = 52046.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.031041 restraints weight = 39353.737| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 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 = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17940 Z= 0.246 Angle : 0.739 14.152 24302 Z= 0.373 Chirality : 0.048 0.656 2689 Planarity : 0.004 0.044 3140 Dihedral : 6.131 39.335 2442 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.34 % Allowed : 16.46 % Favored : 81.20 % 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: -2.69 (0.16), residues: 2202 helix: -0.76 (0.25), residues: 360 sheet: -1.88 (0.20), residues: 615 loop : -2.06 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1577 TYR 0.021 0.002 TYR F 150 PHE 0.020 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/Z covalent geometry : bond 0.00511 / 0.25 (17908) covalent geometry : angle 0.72279 / 0.37 (24230) SS BOND : bond 0.00480 / 0.28 ( 24) SS BOND : angle 1.59852 / 1.01 ( 48) hydrogen bonds : bond 0.05055 / 3.28 ( 643) hydrogen bonds : angle 7.12469 / 4.99 ( 1731) link_BETA1-4 : bond 0.00384 / 0.20 ( 1) link_BETA1-4 : angle 2.13883 / 1.31 ( 3) link_NAG-ASN : bond 0.00771 / 0.37 ( 7) link_NAG-ASN : angle 4.68793 / 3.73 ( 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 111 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 68 time to evaluate : 0.712 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 540 MET cc_start: 0.8087 (ptt) cc_final: 0.7875 (ptt) REVERT: B 173 MET cc_start: 0.8818 (tpp) cc_final: 0.8586 (mmm) REVERT: C 2795 MET cc_start: 0.8699 (tmm) cc_final: 0.8392 (tmm) REVERT: C 2902 MET cc_start: 0.8029 (tpp) cc_final: 0.7586 (mmt) REVERT: C 3224 MET cc_start: 0.7169 (tpt) cc_final: 0.6791 (tpt) REVERT: E 1583 MET cc_start: 0.9122 (mmm) cc_final: 0.8806 (mmm) REVERT: E 1587 ARG cc_start: 0.9193 (mtt180) cc_final: 0.8950 (ptp-110) REVERT: G 134 MET cc_start: 0.9254 (ttt) cc_final: 0.9020 (ttt) REVERT: G 141 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8938 (mm) REVERT: H 0 MET cc_start: 0.8043 (ppp) cc_final: 0.7823 (ppp) REVERT: I 21 MET cc_start: 0.9090 (mpp) cc_final: 0.8556 (tmm) REVERT: I 133 MET cc_start: 0.6748 (tpt) cc_final: 0.5539 (mtt) outliers start: 43 outliers final: 26 residues processed: 108 average time/residue: 0.1117 time to fit residues: 19.9211 Evaluate side-chains 91 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain A residue 358 VAL 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 74 ASN 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 311 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 3012 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 12 VAL 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: 9.9990 chunk 52 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 204 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 212 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN C2706 HIS C2959 GLN C3280 GLN D1777 GLN F 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.039269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.028897 restraints weight = 346223.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.030301 restraints weight = 134014.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.031241 restraints weight = 73756.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.031854 restraints weight = 48789.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.032277 restraints weight = 36601.483| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 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 = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17940 Z= 0.123 Angle : 0.637 12.352 24302 Z= 0.321 Chirality : 0.046 0.532 2689 Planarity : 0.004 0.044 3140 Dihedral : 5.613 44.521 2440 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.51 % Allowed : 16.46 % Favored : 82.03 % 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: -2.30 (0.17), residues: 2202 helix: -0.36 (0.26), residues: 358 sheet: -1.64 (0.20), residues: 623 loop : -1.82 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 94 TYR 0.017 0.001 TYR G 36 PHE 0.011 0.001 PHE E1601 TRP 0.016 0.001 TRP F 103 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17908) covalent geometry : angle 0.62404 / 0.32 (24230) SS BOND : bond 0.00377 / 0.22 ( 24) SS BOND : angle 1.30232 / 0.83 ( 48) hydrogen bonds : bond 0.04092 / 2.66 ( 643) hydrogen bonds : angle 6.62599 / 4.65 ( 1731) link_BETA1-4 : bond 0.00563 / 0.30 ( 1) link_BETA1-4 : angle 1.08697 / 0.73 ( 3) link_NAG-ASN : bond 0.00870 / 0.41 ( 7) link_NAG-ASN : angle 3.98949 / 3.21 ( 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 106 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.654 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 417 MET cc_start: 0.8352 (tpp) cc_final: 0.8134 (tpp) REVERT: A 433 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8194 (p) REVERT: A 540 MET cc_start: 0.8136 (ptt) cc_final: 0.7888 (ptt) REVERT: C 2783 MET cc_start: 0.9221 (ppp) cc_final: 0.8708 (ppp) REVERT: C 2795 MET cc_start: 0.8428 (tmm) cc_final: 0.7849 (tmm) REVERT: C 2842 MET cc_start: 0.8689 (ttm) cc_final: 0.8225 (ttp) REVERT: C 2902 MET cc_start: 0.7859 (tpp) cc_final: 0.7406 (mmt) REVERT: C 3224 MET cc_start: 0.6984 (tpt) cc_final: 0.6450 (tpt) REVERT: E 1573 MET cc_start: 0.9702 (tpp) cc_final: 0.9451 (tmm) REVERT: E 1574 ASP cc_start: 0.9118 (p0) cc_final: 0.8818 (p0) REVERT: E 1577 ARG cc_start: 0.9498 (mtm110) cc_final: 0.9217 (mtm110) REVERT: E 1578 ASP cc_start: 0.8767 (m-30) cc_final: 0.8520 (m-30) REVERT: E 1583 MET cc_start: 0.9123 (mmm) cc_final: 0.8794 (mmm) REVERT: E 1587 ARG cc_start: 0.9197 (mtt180) cc_final: 0.8968 (ptp-110) REVERT: G 103 LYS cc_start: 0.9134 (tttm) cc_final: 0.8807 (tttp) REVERT: G 134 MET cc_start: 0.9213 (ttt) cc_final: 0.8796 (ttt) REVERT: G 141 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8950 (mm) REVERT: G 154 ASP cc_start: 0.9228 (m-30) cc_final: 0.8995 (t0) REVERT: I 21 MET cc_start: 0.9054 (mpp) cc_final: 0.8518 (tmm) REVERT: I 133 MET cc_start: 0.6472 (tpt) cc_final: 0.5321 (mtt) outliers start: 27 outliers final: 16 residues processed: 104 average time/residue: 0.1304 time to fit residues: 22.0380 Evaluate side-chains 88 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 433 SER 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 311 ILE Chi-restraints excluded: chain B residue 373 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 96 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 0.0010 chunk 139 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 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 C2959 GLN ** D1777 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 = 0.3454 r_free = 0.3454 target = 0.037749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.027554 restraints weight = 355886.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.028838 restraints weight = 143553.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.029679 restraints weight = 81018.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.030249 restraints weight = 54762.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.030633 restraints weight = 41662.381| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 17940 Z= 0.315 Angle : 0.779 13.046 24302 Z= 0.387 Chirality : 0.047 0.609 2689 Planarity : 0.004 0.042 3140 Dihedral : 5.873 38.762 2440 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.86 % Allowed : 16.82 % Favored : 80.31 % 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: -2.43 (0.17), residues: 2202 helix: -0.12 (0.26), residues: 361 sheet: -1.88 (0.19), residues: 623 loop : -1.93 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C3180 TYR 0.017 0.002 TYR F 150 PHE 0.023 0.002 PHE A 354 TRP 0.017 0.002 TRP C2939 HIS 0.007 0.002 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.31 (17908) covalent geometry : angle 0.76764 / 0.38 (24230) SS BOND : bond 0.00516 / 0.27 ( 24) SS BOND : angle 1.35734 / 0.90 ( 48) hydrogen bonds : bond 0.04886 / 3.16 ( 643) hydrogen bonds : angle 6.69422 / 4.68 ( 1731) link_BETA1-4 : bond 0.00008 / 0.00 ( 1) link_BETA1-4 : angle 2.24803 / 1.40 ( 3) link_NAG-ASN : bond 0.00660 / 0.32 ( 7) link_NAG-ASN : angle 4.14207 / 3.38 ( 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 116 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 63 time to evaluate : 0.689 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: A 540 MET cc_start: 0.8134 (ptt) cc_final: 0.7889 (ptt) REVERT: B 172 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 2783 MET cc_start: 0.9204 (ppp) cc_final: 0.8705 (ppp) REVERT: C 2820 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7365 (mm) REVERT: C 2902 MET cc_start: 0.8164 (tpp) cc_final: 0.7697 (mmt) REVERT: C 3224 MET cc_start: 0.7320 (tpt) cc_final: 0.6554 (tpt) REVERT: E 1573 MET cc_start: 0.9688 (tpp) cc_final: 0.9443 (tmm) REVERT: E 1574 ASP cc_start: 0.9155 (p0) cc_final: 0.8872 (p0) REVERT: E 1577 ARG cc_start: 0.9525 (mtm110) cc_final: 0.9226 (mtm110) REVERT: E 1583 MET cc_start: 0.9144 (mmm) cc_final: 0.8882 (mmm) REVERT: G 134 MET cc_start: 0.9205 (ttt) cc_final: 0.8866 (ttt) REVERT: G 154 ASP cc_start: 0.9247 (m-30) cc_final: 0.8943 (t0) REVERT: I 21 MET cc_start: 0.9066 (mpp) cc_final: 0.8661 (tmm) REVERT: I 133 MET cc_start: 0.6606 (tpt) cc_final: 0.5501 (mtt) outliers start: 53 outliers final: 38 residues processed: 113 average time/residue: 0.1102 time to fit residues: 20.6639 Evaluate side-chains 100 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 139 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 172 VAL 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 347 VAL 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 3127 PHE 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 12 VAL 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 152 ILE 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: 8.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3499 r_free = 0.3499 target = 0.038729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.028288 restraints weight = 394777.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.029711 restraints weight = 146040.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.030654 restraints weight = 79252.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.031285 restraints weight = 52144.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.031699 restraints weight = 38809.112| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17940 Z= 0.143 Angle : 0.649 12.926 24302 Z= 0.322 Chirality : 0.046 0.530 2689 Planarity : 0.004 0.042 3140 Dihedral : 5.504 45.659 2440 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.08 % Allowed : 17.76 % Favored : 80.16 % 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: -2.12 (0.17), residues: 2202 helix: 0.18 (0.27), residues: 361 sheet: -1.73 (0.20), residues: 613 loop : -1.73 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 147 TYR 0.019 0.001 TYR F 150 PHE 0.013 0.001 PHE A 354 TRP 0.014 0.001 TRP A 190 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17908) covalent geometry : angle 0.63892 / 0.32 (24230) SS BOND : bond 0.00370 / 0.20 ( 24) SS BOND : angle 1.01528 / 0.65 ( 48) hydrogen bonds : bond 0.04034 / 2.63 ( 643) hydrogen bonds : angle 6.36889 / 4.45 ( 1731) link_BETA1-4 : bond 0.00190 / 0.10 ( 1) link_BETA1-4 : angle 1.59743 / 0.99 ( 3) link_NAG-ASN : bond 0.00731 / 0.35 ( 7) link_NAG-ASN : angle 3.69868 / 3.04 ( 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 110 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.701 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: 0.8106 (ptt) cc_final: 0.7846 (ptt) REVERT: B 172 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8644 (p) REVERT: C 2783 MET cc_start: 0.9262 (ppp) cc_final: 0.8815 (ppp) REVERT: C 2820 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7269 (mm) REVERT: C 2902 MET cc_start: 0.8053 (tpp) cc_final: 0.7554 (mmt) REVERT: C 2984 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8188 (tp40) REVERT: C 3224 MET cc_start: 0.6989 (tpt) cc_final: 0.6327 (tpt) REVERT: E 1573 MET cc_start: 0.9718 (tpp) cc_final: 0.9491 (tmm) REVERT: E 1574 ASP cc_start: 0.9140 (p0) cc_final: 0.8819 (p0) REVERT: E 1577 ARG cc_start: 0.9538 (mtm110) cc_final: 0.9257 (mtm110) REVERT: E 1583 MET cc_start: 0.9145 (mmm) cc_final: 0.8849 (mmp) REVERT: G 103 LYS cc_start: 0.9140 (tttm) cc_final: 0.8780 (tttp) REVERT: G 154 ASP cc_start: 0.9250 (m-30) cc_final: 0.9004 (t0) REVERT: I 21 MET cc_start: 0.9011 (mpp) cc_final: 0.8630 (tmm) REVERT: I 133 MET cc_start: 0.6642 (tpt) cc_final: 0.5611 (mtt) REVERT: I 134 MET cc_start: 0.7605 (ptt) cc_final: 0.7059 (ttt) outliers start: 38 outliers final: 27 residues processed: 109 average time/residue: 0.1132 time to fit residues: 20.5732 Evaluate side-chains 96 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 112 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 172 VAL 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 2984 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 112 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 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 547 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN ** D1777 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 = 0.3420 r_free = 0.3420 target = 0.037035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.027323 restraints weight = 272723.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.028432 restraints weight = 126409.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.029165 restraints weight = 76104.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.029657 restraints weight = 53489.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.029992 restraints weight = 41736.206| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 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 = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 17940 Z= 0.402 Angle : 0.886 14.375 24302 Z= 0.439 Chirality : 0.050 0.650 2689 Planarity : 0.005 0.043 3140 Dihedral : 6.190 39.874 2440 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 2.97 % Allowed : 18.59 % Favored : 78.44 % 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: -2.59 (0.17), residues: 2202 helix: -0.03 (0.25), residues: 361 sheet: -2.08 (0.19), residues: 639 loop : -2.05 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C3180 TYR 0.021 0.002 TYR F 79 PHE 0.024 0.003 PHE A 354 TRP 0.019 0.003 TRP C2939 HIS 0.012 0.002 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.40 (17908) covalent geometry : angle 0.87549 / 0.44 (24230) SS BOND : bond 0.00537 / 0.27 ( 24) SS BOND : angle 1.33068 / 0.82 ( 48) hydrogen bonds : bond 0.05237 / 3.39 ( 643) hydrogen bonds : angle 6.80789 / 4.73 ( 1731) link_BETA1-4 : bond 0.00145 / 0.08 ( 1) link_BETA1-4 : angle 2.96063 / 2.00 ( 3) link_NAG-ASN : bond 0.00700 / 0.35 ( 7) link_NAG-ASN : angle 4.35026 / 3.57 ( 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 117 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 62 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8037 (ptt) cc_final: 0.7806 (ptt) REVERT: B 172 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8719 (p) REVERT: C 2783 MET cc_start: 0.9280 (ppp) cc_final: 0.8485 (ppp) REVERT: C 2795 MET cc_start: 0.8274 (tmm) cc_final: 0.7639 (tmm) REVERT: C 2820 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7242 (mm) REVERT: C 2902 MET cc_start: 0.8218 (tpp) cc_final: 0.7726 (mmt) REVERT: C 3224 MET cc_start: 0.7579 (tpt) cc_final: 0.7195 (tpt) REVERT: E 1583 MET cc_start: 0.9136 (mmm) cc_final: 0.8837 (mmm) REVERT: G 133 MET cc_start: 0.9273 (ptp) cc_final: 0.9025 (ptp) REVERT: I 21 MET cc_start: 0.9099 (mpp) cc_final: 0.8688 (tmm) REVERT: I 133 MET cc_start: 0.6591 (tpt) cc_final: 0.5490 (mtt) outliers start: 55 outliers final: 45 residues processed: 115 average time/residue: 0.1066 time to fit residues: 20.6048 Evaluate side-chains 102 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 55 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 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 172 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 240 VAL 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 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 3127 PHE 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 12 VAL 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 G residue 156 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: 1.9990 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.038576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.028034 restraints weight = 412563.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.029470 restraints weight = 151178.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.030414 restraints weight = 81733.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.031040 restraints weight = 53587.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031462 restraints weight = 39863.843| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17940 Z= 0.145 Angle : 0.677 14.269 24302 Z= 0.334 Chirality : 0.046 0.554 2689 Planarity : 0.004 0.046 3140 Dihedral : 5.605 47.918 2440 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.34 % Allowed : 19.22 % Favored : 78.44 % 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: -2.15 (0.17), residues: 2202 helix: 0.43 (0.27), residues: 361 sheet: -1.90 (0.19), residues: 641 loop : -1.72 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1577 TYR 0.014 0.001 TYR C3163 PHE 0.014 0.001 PHE A 354 TRP 0.018 0.002 TRP A 29 HIS 0.004 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17908) covalent geometry : angle 0.66584 / 0.33 (24230) SS BOND : bond 0.00432 / 0.27 ( 24) SS BOND : angle 1.29105 / 0.72 ( 48) hydrogen bonds : bond 0.03985 / 2.61 ( 643) hydrogen bonds : angle 6.33360 / 4.41 ( 1731) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 1.97534 / 1.14 ( 3) link_NAG-ASN : bond 0.00696 / 0.34 ( 7) link_NAG-ASN : angle 3.75182 / 3.08 ( 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 113 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 70 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8075 (ptt) cc_final: 0.7816 (ptt) REVERT: B 172 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8680 (p) REVERT: B 229 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: C 2783 MET cc_start: 0.9295 (ppp) cc_final: 0.8610 (ppp) REVERT: C 2820 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (mm) REVERT: C 2984 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8308 (tp40) REVERT: C 3125 MET cc_start: 0.8942 (mmt) cc_final: 0.8733 (mmt) REVERT: C 3224 MET cc_start: 0.7157 (tpt) cc_final: 0.6406 (tpt) REVERT: E 1574 ASP cc_start: 0.9375 (p0) cc_final: 0.9123 (p0) REVERT: E 1577 ARG cc_start: 0.9479 (mtm110) cc_final: 0.9195 (mtm110) REVERT: E 1583 MET cc_start: 0.9127 (mmm) cc_final: 0.8824 (mmp) REVERT: G 78 MET cc_start: 0.8071 (tpt) cc_final: 0.7003 (tpp) REVERT: G 103 LYS cc_start: 0.9176 (tttm) cc_final: 0.8872 (tttp) REVERT: G 133 MET cc_start: 0.9286 (ptp) cc_final: 0.9032 (ptp) REVERT: G 154 ASP cc_start: 0.9327 (m-30) cc_final: 0.9040 (t0) REVERT: I 21 MET cc_start: 0.9007 (mpp) cc_final: 0.8620 (tmm) REVERT: I 133 MET cc_start: 0.6925 (tpt) cc_final: 0.5919 (mtt) REVERT: I 134 MET cc_start: 0.7630 (ptt) cc_final: 0.7103 (ttt) outliers start: 43 outliers final: 32 residues processed: 111 average time/residue: 0.1148 time to fit residues: 20.7373 Evaluate side-chains 101 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 172 VAL 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 B residue 436 VAL 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 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: 7.9990 chunk 188 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 211 optimal weight: 0.1980 chunk 184 optimal weight: 8.9990 chunk 39 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 346 ASN C2959 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.038676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.028463 restraints weight = 339150.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.030288 restraints weight = 139833.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031106 restraints weight = 62691.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.031500 restraints weight = 39710.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.031630 restraints weight = 35109.996| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17940 Z= 0.156 Angle : 0.688 14.818 24302 Z= 0.337 Chirality : 0.046 0.545 2689 Planarity : 0.004 0.048 3140 Dihedral : 5.480 48.636 2440 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.19 % Allowed : 19.69 % Favored : 78.12 % 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: 0.54 (0.27), residues: 361 sheet: -1.67 (0.20), residues: 609 loop : -1.68 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1577 TYR 0.013 0.001 TYR C3163 PHE 0.017 0.001 PHE A 354 TRP 0.017 0.002 TRP A 190 HIS 0.003 0.001 HIS C2706 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (17908) covalent geometry : angle 0.67696 / 0.33 (24230) SS BOND : bond 0.00409 / 0.25 ( 24) SS BOND : angle 1.62714 / 0.99 ( 48) hydrogen bonds : bond 0.03913 / 2.55 ( 643) hydrogen bonds : angle 6.18367 / 4.30 ( 1731) link_BETA1-4 : bond 0.00262 / 0.14 ( 1) link_BETA1-4 : angle 1.65664 / 0.96 ( 3) link_NAG-ASN : bond 0.00678 / 0.33 ( 7) link_NAG-ASN : angle 3.56954 / 2.98 ( 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 106 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.665 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: A 144 MET cc_start: 0.8589 (tpp) cc_final: 0.8161 (mmt) REVERT: A 540 MET cc_start: 0.8068 (ptt) cc_final: 0.7828 (ptt) REVERT: C 2783 MET cc_start: 0.9279 (ppp) cc_final: 0.8704 (ppp) REVERT: C 2820 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7337 (mm) REVERT: C 2902 MET cc_start: 0.7986 (tpp) cc_final: 0.7535 (mmt) REVERT: C 2984 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8255 (tp40) REVERT: C 3224 MET cc_start: 0.7259 (tpt) cc_final: 0.6501 (tpt) REVERT: E 1574 ASP cc_start: 0.9348 (p0) cc_final: 0.9116 (p0) REVERT: E 1577 ARG cc_start: 0.9530 (mtm110) cc_final: 0.9284 (mtm110) REVERT: E 1583 MET cc_start: 0.9111 (mmm) cc_final: 0.8811 (mmm) REVERT: G 78 MET cc_start: 0.8076 (tpt) cc_final: 0.7046 (tpp) REVERT: G 154 ASP cc_start: 0.9385 (m-30) cc_final: 0.9101 (t0) REVERT: I 21 MET cc_start: 0.9004 (mpp) cc_final: 0.8608 (tmm) REVERT: I 133 MET cc_start: 0.6840 (tpt) cc_final: 0.5893 (mtt) REVERT: I 134 MET cc_start: 0.7691 (ptt) cc_final: 0.7180 (ttt) outliers start: 40 outliers final: 35 residues processed: 103 average time/residue: 0.1118 time to fit residues: 18.7383 Evaluate side-chains 101 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 419 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 74 ASN 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 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 2859 VAL 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 3127 PHE 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 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: 3.9990 chunk 17 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN ** C3280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.037934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.027781 restraints weight = 315232.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.029045 restraints weight = 132438.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.029880 restraints weight = 75960.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.030437 restraints weight = 51777.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.030817 restraints weight = 39625.499| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 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 = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17940 Z= 0.255 Angle : 0.757 14.792 24302 Z= 0.371 Chirality : 0.047 0.580 2689 Planarity : 0.004 0.047 3140 Dihedral : 5.672 47.076 2440 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.19 % Allowed : 19.64 % Favored : 78.18 % 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: -2.13 (0.17), residues: 2202 helix: 0.40 (0.27), residues: 363 sheet: -1.83 (0.20), residues: 633 loop : -1.75 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E1577 TYR 0.014 0.002 TYR C3163 PHE 0.023 0.002 PHE A 354 TRP 0.013 0.002 TRP C2939 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (17908) covalent geometry : angle 0.74579 / 0.37 (24230) SS BOND : bond 0.00465 / 0.26 ( 24) SS BOND : angle 1.66133 / 1.07 ( 48) hydrogen bonds : bond 0.04257 / 2.76 ( 643) hydrogen bonds : angle 6.30131 / 4.37 ( 1731) link_BETA1-4 : bond 0.00290 / 0.15 ( 1) link_BETA1-4 : angle 2.05507 / 1.21 ( 3) link_NAG-ASN : bond 0.00650 / 0.32 ( 7) link_NAG-ASN : angle 3.72924 / 3.14 ( 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 99 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 540 MET cc_start: 0.8085 (ptt) cc_final: 0.7873 (ptt) REVERT: C 2783 MET cc_start: 0.9289 (ppp) cc_final: 0.8691 (ppp) REVERT: C 2820 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7346 (mm) REVERT: C 2902 MET cc_start: 0.8106 (tpp) cc_final: 0.7846 (tpp) REVERT: C 2984 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8171 (tp40) REVERT: C 3125 MET cc_start: 0.8904 (mmt) cc_final: 0.8665 (mmt) REVERT: C 3224 MET cc_start: 0.7311 (tpt) cc_final: 0.6552 (tpt) REVERT: E 1574 ASP cc_start: 0.9354 (p0) cc_final: 0.9139 (p0) REVERT: E 1577 ARG cc_start: 0.9534 (mtm110) cc_final: 0.9290 (mtm110) REVERT: E 1583 MET cc_start: 0.9098 (mmm) cc_final: 0.8813 (mmp) REVERT: G 78 MET cc_start: 0.8179 (tpt) cc_final: 0.7945 (tpp) REVERT: G 154 ASP cc_start: 0.9334 (m-30) cc_final: 0.9015 (t0) REVERT: I 21 MET cc_start: 0.9029 (mpp) cc_final: 0.8679 (tmm) REVERT: I 133 MET cc_start: 0.6648 (tpt) cc_final: 0.5704 (mtt) outliers start: 40 outliers final: 36 residues processed: 99 average time/residue: 0.1172 time to fit residues: 19.3111 Evaluate side-chains 96 residues out of total 1916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 347 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 543 THR Chi-restraints excluded: chain B residue 55 CYS 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 188 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 B residue 436 VAL Chi-restraints excluded: chain C residue 2820 ILE Chi-restraints excluded: chain C residue 2859 VAL 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 3127 PHE 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 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: 6.9990 chunk 204 optimal weight: 30.0000 chunk 141 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2959 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.038466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.028103 restraints weight = 357745.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.029466 restraints weight = 140456.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.030361 restraints weight = 77950.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.030956 restraints weight = 51984.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.031361 restraints weight = 39178.668| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17940 Z= 0.183 Angle : 0.709 15.705 24302 Z= 0.347 Chirality : 0.047 0.552 2689 Planarity : 0.004 0.048 3140 Dihedral : 5.553 49.587 2440 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.34 % Allowed : 19.79 % Favored : 77.86 % 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: -2.01 (0.17), residues: 2202 helix: 0.63 (0.27), residues: 355 sheet: -1.80 (0.19), residues: 654 loop : -1.66 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1577 TYR 0.013 0.001 TYR C3163 PHE 0.018 0.002 PHE A 354 TRP 0.014 0.002 TRP A 190 HIS 0.004 0.001 HIS B 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (17908) covalent geometry : angle 0.69866 / 0.34 (24230) SS BOND : bond 0.00429 / 0.25 ( 24) SS BOND : angle 1.47621 / 0.93 ( 48) hydrogen bonds : bond 0.03940 / 2.56 ( 643) hydrogen bonds : angle 6.16976 / 4.28 ( 1731) link_BETA1-4 : bond 0.00217 / 0.11 ( 1) link_BETA1-4 : angle 1.79855 / 1.07 ( 3) link_NAG-ASN : bond 0.00636 / 0.31 ( 7) link_NAG-ASN : angle 3.53907 / 3.00 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4624.68 seconds wall clock time: 80 minutes 9.65 seconds (4809.65 seconds total)