Starting phenix.real_space_refine on Mon Aug 5 08:40:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qrh_18614/08_2024/8qrh_18614.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 8220 2.51 5 N 2274 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12951 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "B" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "C" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.85, per 1000 atoms: 0.61 Number of scatterers: 12951 At special positions: 0 Unit cell: (114.75, 195.075, 94.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2376 8.00 N 2274 7.00 C 8220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 338 " distance=2.02 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 338 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 500 " - " ASN A 154 " " NAG B 500 " - " ASN B 154 " " NAG C 500 " - " ASN C 154 " Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.4 seconds 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 27 sheets defined 31.8% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.618A pdb=" N HIS A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.595A pdb=" N HIS A 104 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 397 through 417 removed outlier: 3.753A pdb=" N VAL A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.591A pdb=" N TRP A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 473 through 476 removed outlier: 4.378A pdb=" N MET A 476 " --> pdb=" O ASN A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.051A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 397 through 417 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 427 through 450 removed outlier: 3.995A pdb=" N THR B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 474 through 492 removed outlier: 4.121A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.508A pdb=" N THR C 4 " --> pdb=" O SER C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.661A pdb=" N HIS C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 397 through 420 removed outlier: 3.591A pdb=" N THR C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 448 removed outlier: 4.232A pdb=" N VAL C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 470 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.590A pdb=" N SER D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'E' and resid 26 through 54 removed outlier: 4.017A pdb=" N THR E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.805A pdb=" N ARG E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 20 through 28 removed outlier: 4.161A pdb=" N ARG F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 39 through 54 Processing helix chain 'F' and resid 58 through 71 removed outlier: 5.689A pdb=" N LEU F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.806A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A 140 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 48 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 138 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.806A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 212 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 58 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 129 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 54 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 73 removed outlier: 4.287A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 114 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 112 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.172A pdb=" N GLU A 329 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 317 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 327 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 10 removed outlier: 6.965A pdb=" N THR B 140 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 48 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B 138 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.433A pdb=" N ALA B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 58 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 129 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 72 removed outlier: 4.332A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 242 through 244 Processing sheet with id=AB7, first strand: chain 'B' and resid 312 through 320 removed outlier: 5.568A pdb=" N TRP B 314 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 331 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 327 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB9, first strand: chain 'B' and resid 342 through 346 Processing sheet with id=AC1, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.940A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 12 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C 140 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE C 48 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 138 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.940A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 12 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C 212 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 58 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 129 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 20 through 26 removed outlier: 4.641A pdb=" N THR C 289 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 63 through 72 removed outlier: 4.342A pdb=" N THR C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS C 116 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 70 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 114 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 112 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.920A pdb=" N GLY C 180 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 242 through 244 Processing sheet with id=AC7, first strand: chain 'C' and resid 312 through 320 removed outlier: 6.452A pdb=" N GLU C 329 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE C 317 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 327 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC9, first strand: chain 'C' and resid 342 through 346 601 hydrogen bonds defined for protein. 1605 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: 4.60 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4214 1.34 - 1.46: 3032 1.46 - 1.59: 5870 1.59 - 1.71: 0 1.71 - 1.83: 123 Bond restraints: 13239 Sorted by residual: bond pdb=" CA GLY C 180 " pdb=" C GLY C 180 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.77e+00 bond pdb=" C1 NAG B 500 " pdb=" O5 NAG B 500 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N GLY C 180 " pdb=" CA GLY C 180 " ideal model delta sigma weight residual 1.464 1.450 0.014 1.12e-02 7.97e+03 1.67e+00 bond pdb=" C5 NAG C 500 " pdb=" O5 NAG C 500 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 500 " pdb=" O5 NAG C 500 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 ... (remaining 13234 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.55: 285 105.55 - 112.71: 7307 112.71 - 119.87: 4320 119.87 - 127.04: 5842 127.04 - 134.20: 225 Bond angle restraints: 17979 Sorted by residual: angle pdb=" N ARG E 40 " pdb=" CA ARG E 40 " pdb=" C ARG E 40 " ideal model delta sigma weight residual 110.80 118.46 -7.66 2.13e+00 2.20e-01 1.29e+01 angle pdb=" C LEU B 448 " pdb=" N PHE B 449 " pdb=" CA PHE B 449 " ideal model delta sigma weight residual 120.68 126.32 -5.64 1.70e+00 3.46e-01 1.10e+01 angle pdb=" N GLY C 180 " pdb=" CA GLY C 180 " pdb=" C GLY C 180 " ideal model delta sigma weight residual 111.67 114.69 -3.02 9.20e-01 1.18e+00 1.08e+01 angle pdb=" CA TRP D 19 " pdb=" CB TRP D 19 " pdb=" CG TRP D 19 " ideal model delta sigma weight residual 113.60 119.46 -5.86 1.90e+00 2.77e-01 9.51e+00 angle pdb=" CA LYS B 457 " pdb=" CB LYS B 457 " pdb=" CG LYS B 457 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 ... (remaining 17974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7342 17.79 - 35.58: 424 35.58 - 53.37: 58 53.37 - 71.16: 20 71.16 - 88.94: 7 Dihedral angle restraints: 7851 sinusoidal: 3102 harmonic: 4749 Sorted by residual: dihedral pdb=" CA GLY C 427 " pdb=" C GLY C 427 " pdb=" N GLY C 428 " pdb=" CA GLY C 428 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASN E 39 " pdb=" C ASN E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASN D 39 " pdb=" C ASN D 39 " pdb=" N ARG D 40 " pdb=" CA ARG D 40 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 7848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1275 0.036 - 0.071: 566 0.071 - 0.107: 161 0.107 - 0.143: 78 0.143 - 0.178: 5 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CB ILE B 33 " pdb=" CA ILE B 33 " pdb=" CG1 ILE B 33 " pdb=" CG2 ILE B 33 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ASN E 39 " pdb=" N ASN E 39 " pdb=" C ASN E 39 " pdb=" CB ASN E 39 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA HIS A 260 " pdb=" N HIS A 260 " pdb=" C HIS A 260 " pdb=" CB HIS A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2082 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " 0.346 9.50e-02 1.11e+02 1.56e-01 1.79e+01 pdb=" NE ARG A 412 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 414 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C THR C 414 " -0.068 2.00e-02 2.50e+03 pdb=" O THR C 414 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 415 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 413 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU A 413 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU A 413 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 414 " 0.022 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2395 2.78 - 3.31: 12361 3.31 - 3.84: 19975 3.84 - 4.37: 23233 4.37 - 4.90: 40823 Nonbonded interactions: 98787 Sorted by model distance: nonbonded pdb=" O ALA B 426 " pdb=" OG1 THR B 431 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU B 411 " pdb=" NH2 ARG D 15 " model vdw 2.316 3.120 nonbonded pdb=" O LEU E 54 " pdb=" NE ARG E 60 " model vdw 2.339 3.120 nonbonded pdb=" O SER F 24 " pdb=" OG1 THR F 27 " model vdw 2.359 3.040 nonbonded pdb=" O PRO B 474 " pdb=" OG SER B 477 " model vdw 2.379 3.040 ... (remaining 98782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.340 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13239 Z= 0.184 Angle : 0.718 7.661 17979 Z= 0.422 Chirality : 0.046 0.178 2085 Planarity : 0.008 0.156 2256 Dihedral : 12.207 88.944 4761 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1677 helix: -0.19 (0.22), residues: 411 sheet: -0.53 (0.22), residues: 486 loop : -0.62 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 19 HIS 0.006 0.001 HIS A 229 PHE 0.033 0.002 PHE A 480 TYR 0.014 0.003 TYR A 384 ARG 0.031 0.003 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.384 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 101 TRP cc_start: 0.6129 (m100) cc_final: 0.5220 (m100) REVERT: A 251 LYS cc_start: 0.8399 (mttt) cc_final: 0.8182 (tptt) REVERT: A 476 MET cc_start: 0.3698 (mmt) cc_final: 0.2739 (mmt) REVERT: B 87 GLN cc_start: 0.7292 (mt0) cc_final: 0.6881 (mp10) REVERT: B 306 MET cc_start: 0.7705 (mmm) cc_final: 0.7419 (mmt) REVERT: B 316 ARG cc_start: 0.7456 (ttt180) cc_final: 0.4952 (tpp80) REVERT: B 404 GLN cc_start: 0.8053 (tp40) cc_final: 0.7563 (tm-30) REVERT: C 8 ASN cc_start: 0.8254 (t0) cc_final: 0.7219 (t0) REVERT: C 41 MET cc_start: 0.9013 (mmt) cc_final: 0.8062 (mmt) REVERT: C 87 GLN cc_start: 0.6680 (mt0) cc_final: 0.6130 (mp10) REVERT: C 252 MET cc_start: 0.8429 (ttt) cc_final: 0.8177 (ttm) REVERT: C 306 MET cc_start: 0.8649 (mmt) cc_final: 0.8337 (mmt) REVERT: E 52 LEU cc_start: 0.9508 (mt) cc_final: 0.9225 (mt) REVERT: F 7 HIS cc_start: 0.6800 (t-90) cc_final: 0.5181 (m-70) REVERT: F 19 TRP cc_start: 0.7321 (m100) cc_final: 0.6713 (m-10) REVERT: F 41 LEU cc_start: 0.9037 (mt) cc_final: 0.8750 (pt) REVERT: F 46 MET cc_start: 0.9498 (mmm) cc_final: 0.9138 (mmp) REVERT: F 50 VAL cc_start: 0.9528 (t) cc_final: 0.9273 (p) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2650 time to fit residues: 119.7445 Evaluate side-chains 200 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 30.0000 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 80 optimal weight: 0.0670 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 221 ASN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 375 GLN B 419 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN E 7 HIS F 28 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13239 Z= 0.309 Angle : 0.691 9.082 17979 Z= 0.367 Chirality : 0.047 0.204 2085 Planarity : 0.004 0.042 2256 Dihedral : 6.529 45.596 1845 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.22 % Allowed : 8.23 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1677 helix: 1.04 (0.25), residues: 400 sheet: -0.31 (0.23), residues: 467 loop : -0.29 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 101 HIS 0.007 0.001 HIS C 229 PHE 0.023 0.002 PHE A 480 TYR 0.031 0.002 TYR A 304 ARG 0.008 0.001 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8670 (mtpp) REVERT: A 251 LYS cc_start: 0.8562 (mttt) cc_final: 0.8302 (tptt) REVERT: A 255 TYR cc_start: 0.8543 (m-80) cc_final: 0.8329 (m-80) REVERT: A 394 GLN cc_start: 0.8583 (tp40) cc_final: 0.8303 (tp40) REVERT: B 87 GLN cc_start: 0.7242 (mt0) cc_final: 0.6853 (mp10) REVERT: B 404 GLN cc_start: 0.8014 (tp40) cc_final: 0.7523 (tm-30) REVERT: B 478 MET cc_start: 0.8701 (mpp) cc_final: 0.8395 (ppp) REVERT: C 87 GLN cc_start: 0.7108 (mt0) cc_final: 0.6807 (mp10) REVERT: C 367 ASN cc_start: 0.8156 (t0) cc_final: 0.7927 (t0) REVERT: C 374 MET cc_start: 0.8009 (mtp) cc_final: 0.7788 (mtp) REVERT: E 39 ASN cc_start: 0.7964 (t0) cc_final: 0.7302 (t0) REVERT: E 46 MET cc_start: 0.8382 (ptm) cc_final: 0.8156 (ptt) REVERT: E 48 THR cc_start: 0.9283 (p) cc_final: 0.8984 (t) REVERT: E 52 LEU cc_start: 0.9470 (mt) cc_final: 0.9073 (mt) REVERT: F 7 HIS cc_start: 0.7065 (t-90) cc_final: 0.5322 (m-70) REVERT: F 46 MET cc_start: 0.9487 (mmm) cc_final: 0.9221 (mmp) outliers start: 17 outliers final: 12 residues processed: 241 average time/residue: 0.2388 time to fit residues: 84.0144 Evaluate side-chains 208 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 152 optimal weight: 0.0170 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN C 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13239 Z= 0.304 Angle : 0.654 10.022 17979 Z= 0.344 Chirality : 0.045 0.167 2085 Planarity : 0.004 0.044 2256 Dihedral : 6.105 47.953 1845 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.43 % Allowed : 11.52 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1677 helix: 1.22 (0.26), residues: 388 sheet: -0.31 (0.24), residues: 467 loop : -0.29 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 35 HIS 0.006 0.001 HIS C 229 PHE 0.023 0.002 PHE B 454 TYR 0.041 0.002 TYR A 304 ARG 0.005 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLN cc_start: 0.8435 (mm110) cc_final: 0.8140 (mm110) REVERT: A 251 LYS cc_start: 0.8607 (mttt) cc_final: 0.8388 (tptt) REVERT: A 476 MET cc_start: 0.4770 (mmt) cc_final: 0.4303 (mmp) REVERT: B 87 GLN cc_start: 0.7273 (mt0) cc_final: 0.6880 (mp10) REVERT: B 243 GLU cc_start: 0.7518 (tp30) cc_final: 0.7292 (tp30) REVERT: B 404 GLN cc_start: 0.8046 (tp40) cc_final: 0.7527 (tm-30) REVERT: C 86 HIS cc_start: 0.7780 (m-70) cc_final: 0.7507 (m-70) REVERT: C 252 MET cc_start: 0.8763 (ttt) cc_final: 0.8469 (ttm) REVERT: C 367 ASN cc_start: 0.8130 (t0) cc_final: 0.7826 (t0) REVERT: C 374 MET cc_start: 0.8084 (mtp) cc_final: 0.7851 (mtp) REVERT: D 46 MET cc_start: 0.7948 (mmm) cc_final: 0.7366 (mmm) REVERT: E 35 TRP cc_start: 0.8544 (t-100) cc_final: 0.8193 (t-100) REVERT: E 39 ASN cc_start: 0.8281 (t0) cc_final: 0.7587 (t0) REVERT: E 40 ARG cc_start: 0.6431 (ptp-170) cc_final: 0.6092 (ptp-170) REVERT: E 46 MET cc_start: 0.8482 (ptm) cc_final: 0.8277 (ptt) REVERT: E 52 LEU cc_start: 0.9457 (mt) cc_final: 0.9149 (mt) REVERT: E 64 LEU cc_start: 0.9729 (mt) cc_final: 0.9266 (pp) REVERT: F 7 HIS cc_start: 0.7079 (t-90) cc_final: 0.5315 (m-70) REVERT: F 46 MET cc_start: 0.9479 (mmm) cc_final: 0.9235 (mmp) outliers start: 20 outliers final: 16 residues processed: 218 average time/residue: 0.2328 time to fit residues: 74.8266 Evaluate side-chains 204 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13239 Z= 0.376 Angle : 0.659 9.144 17979 Z= 0.349 Chirality : 0.046 0.165 2085 Planarity : 0.004 0.046 2256 Dihedral : 6.076 51.895 1845 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 12.52 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1677 helix: 1.25 (0.26), residues: 388 sheet: -0.44 (0.24), residues: 465 loop : -0.53 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 101 HIS 0.007 0.001 HIS A 282 PHE 0.016 0.002 PHE B 449 TYR 0.031 0.002 TYR A 304 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.8602 (mttt) cc_final: 0.8375 (tptt) REVERT: A 486 LEU cc_start: 0.7430 (mt) cc_final: 0.6465 (tt) REVERT: B 87 GLN cc_start: 0.7344 (mt0) cc_final: 0.6914 (mp10) REVERT: B 243 GLU cc_start: 0.7578 (tp30) cc_final: 0.7329 (tp30) REVERT: B 404 GLN cc_start: 0.7933 (tp40) cc_final: 0.7432 (tm-30) REVERT: B 478 MET cc_start: 0.8331 (mpp) cc_final: 0.7874 (ppp) REVERT: C 86 HIS cc_start: 0.7873 (m-70) cc_final: 0.7598 (m-70) REVERT: C 87 GLN cc_start: 0.7204 (mp10) cc_final: 0.6965 (mp10) REVERT: C 252 MET cc_start: 0.8780 (ttt) cc_final: 0.8385 (ttm) REVERT: C 367 ASN cc_start: 0.8168 (t0) cc_final: 0.7960 (t0) REVERT: D 46 MET cc_start: 0.7935 (mmm) cc_final: 0.7333 (mmm) REVERT: E 35 TRP cc_start: 0.8491 (t-100) cc_final: 0.8189 (t-100) REVERT: E 39 ASN cc_start: 0.8619 (t0) cc_final: 0.8007 (t0) REVERT: E 40 ARG cc_start: 0.6528 (ptp-170) cc_final: 0.6110 (ptp-170) REVERT: E 52 LEU cc_start: 0.9465 (mt) cc_final: 0.9160 (mt) REVERT: E 64 LEU cc_start: 0.9725 (mt) cc_final: 0.9269 (pp) REVERT: F 7 HIS cc_start: 0.7097 (t-90) cc_final: 0.5346 (m-70) REVERT: F 46 MET cc_start: 0.9480 (mmm) cc_final: 0.9242 (mmp) outliers start: 37 outliers final: 32 residues processed: 226 average time/residue: 0.2572 time to fit residues: 85.4618 Evaluate side-chains 224 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 0.0040 chunk 40 optimal weight: 9.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13239 Z= 0.208 Angle : 0.599 10.283 17979 Z= 0.311 Chirality : 0.043 0.154 2085 Planarity : 0.004 0.055 2256 Dihedral : 5.705 46.713 1845 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.15 % Allowed : 14.31 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1677 helix: 1.14 (0.25), residues: 404 sheet: -0.32 (0.24), residues: 469 loop : -0.52 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 101 HIS 0.004 0.001 HIS A 282 PHE 0.015 0.001 PHE B 449 TYR 0.029 0.002 TYR A 304 ARG 0.005 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 204 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.8625 (mttt) cc_final: 0.8425 (tptt) REVERT: A 486 LEU cc_start: 0.7558 (mt) cc_final: 0.6621 (tt) REVERT: B 243 GLU cc_start: 0.7561 (tp30) cc_final: 0.7332 (tp30) REVERT: B 404 GLN cc_start: 0.7945 (tp40) cc_final: 0.7485 (tm-30) REVERT: C 87 GLN cc_start: 0.7047 (mp10) cc_final: 0.6665 (mp10) REVERT: C 252 MET cc_start: 0.8767 (ttt) cc_final: 0.8470 (ttm) REVERT: C 367 ASN cc_start: 0.8227 (t0) cc_final: 0.7989 (t0) REVERT: D 46 MET cc_start: 0.7935 (mmm) cc_final: 0.7497 (mmm) REVERT: E 35 TRP cc_start: 0.8444 (t-100) cc_final: 0.8197 (t-100) REVERT: E 39 ASN cc_start: 0.8672 (t0) cc_final: 0.8290 (t0) REVERT: E 40 ARG cc_start: 0.6658 (ptp-170) cc_final: 0.6248 (ptp-170) REVERT: E 52 LEU cc_start: 0.9420 (mt) cc_final: 0.9109 (mt) REVERT: E 64 LEU cc_start: 0.9693 (mt) cc_final: 0.9257 (pp) REVERT: F 7 HIS cc_start: 0.7133 (t-90) cc_final: 0.5328 (m-70) REVERT: F 46 MET cc_start: 0.9482 (mmm) cc_final: 0.9238 (mmp) outliers start: 30 outliers final: 23 residues processed: 223 average time/residue: 0.2364 time to fit residues: 77.3279 Evaluate side-chains 217 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.0980 chunk 146 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 375 GLN C 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13239 Z= 0.266 Angle : 0.613 10.295 17979 Z= 0.318 Chirality : 0.044 0.153 2085 Planarity : 0.004 0.053 2256 Dihedral : 5.609 48.077 1845 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.72 % Allowed : 14.38 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.20), residues: 1677 helix: 1.18 (0.26), residues: 405 sheet: -0.41 (0.24), residues: 467 loop : -0.59 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 51 HIS 0.006 0.001 HIS A 282 PHE 0.016 0.002 PHE B 454 TYR 0.029 0.002 TYR A 304 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LYS cc_start: 0.8639 (mttt) cc_final: 0.8430 (tptt) REVERT: A 486 LEU cc_start: 0.7459 (mt) cc_final: 0.6486 (tt) REVERT: B 87 GLN cc_start: 0.7583 (mt0) cc_final: 0.7360 (mp10) REVERT: B 404 GLN cc_start: 0.7945 (tp40) cc_final: 0.7463 (tm-30) REVERT: C 252 MET cc_start: 0.8764 (ttt) cc_final: 0.8420 (ttm) REVERT: C 367 ASN cc_start: 0.8227 (t0) cc_final: 0.8014 (t0) REVERT: D 46 MET cc_start: 0.7999 (mmm) cc_final: 0.7571 (mmm) REVERT: E 35 TRP cc_start: 0.8422 (t-100) cc_final: 0.8214 (t-100) REVERT: E 39 ASN cc_start: 0.8677 (t0) cc_final: 0.8221 (t0) REVERT: E 40 ARG cc_start: 0.6666 (ptp-170) cc_final: 0.6287 (ptp-170) REVERT: E 52 LEU cc_start: 0.9365 (mt) cc_final: 0.9053 (mt) REVERT: E 64 LEU cc_start: 0.9691 (mt) cc_final: 0.9258 (pp) REVERT: F 7 HIS cc_start: 0.7143 (t-90) cc_final: 0.5348 (m-70) REVERT: F 46 MET cc_start: 0.9485 (mmm) cc_final: 0.9255 (mmp) outliers start: 38 outliers final: 30 residues processed: 228 average time/residue: 0.2275 time to fit residues: 76.8176 Evaluate side-chains 225 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 HIS B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13239 Z= 0.421 Angle : 0.695 13.401 17979 Z= 0.359 Chirality : 0.047 0.161 2085 Planarity : 0.004 0.060 2256 Dihedral : 5.872 53.338 1845 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.00 % Allowed : 15.02 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1677 helix: 1.08 (0.26), residues: 401 sheet: -0.62 (0.24), residues: 462 loop : -0.78 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 101 HIS 0.007 0.001 HIS A 282 PHE 0.017 0.002 PHE B 449 TYR 0.035 0.002 TYR A 304 ARG 0.007 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8452 (m-30) cc_final: 0.8228 (t0) REVERT: A 251 LYS cc_start: 0.8649 (mttt) cc_final: 0.8379 (tptt) REVERT: B 87 GLN cc_start: 0.7790 (mt0) cc_final: 0.7459 (mp10) REVERT: B 243 GLU cc_start: 0.7636 (tp30) cc_final: 0.7409 (tp30) REVERT: B 404 GLN cc_start: 0.8013 (tp40) cc_final: 0.7547 (tm-30) REVERT: C 69 LYS cc_start: 0.8779 (mttm) cc_final: 0.8549 (mttm) REVERT: C 87 GLN cc_start: 0.7592 (mp10) cc_final: 0.6979 (mp10) REVERT: C 367 ASN cc_start: 0.8279 (t0) cc_final: 0.8032 (t0) REVERT: D 46 MET cc_start: 0.8210 (mmm) cc_final: 0.7798 (mmm) REVERT: E 35 TRP cc_start: 0.8488 (t-100) cc_final: 0.8272 (t-100) REVERT: E 39 ASN cc_start: 0.8614 (t0) cc_final: 0.8092 (t0) REVERT: E 40 ARG cc_start: 0.6709 (ptp-170) cc_final: 0.6340 (ptp-170) REVERT: E 52 LEU cc_start: 0.9399 (mt) cc_final: 0.9126 (mt) REVERT: E 64 LEU cc_start: 0.9694 (mt) cc_final: 0.9264 (pp) REVERT: F 7 HIS cc_start: 0.7112 (t-90) cc_final: 0.5384 (m-70) outliers start: 42 outliers final: 33 residues processed: 229 average time/residue: 0.2331 time to fit residues: 79.1083 Evaluate side-chains 226 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 31 optimal weight: 0.1980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13239 Z= 0.275 Angle : 0.658 16.252 17979 Z= 0.332 Chirality : 0.044 0.160 2085 Planarity : 0.004 0.061 2256 Dihedral : 5.702 50.066 1845 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.79 % Allowed : 15.74 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1677 helix: 1.16 (0.26), residues: 401 sheet: -0.57 (0.24), residues: 465 loop : -0.73 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 51 HIS 0.006 0.001 HIS A 282 PHE 0.014 0.002 PHE B 332 TYR 0.033 0.002 TYR A 304 ARG 0.007 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8416 (m-30) cc_final: 0.8202 (t0) REVERT: A 251 LYS cc_start: 0.8655 (mttt) cc_final: 0.8392 (tptt) REVERT: A 319 THR cc_start: 0.9139 (m) cc_final: 0.8842 (p) REVERT: A 471 MET cc_start: 0.5797 (mmt) cc_final: 0.4995 (mmt) REVERT: B 87 GLN cc_start: 0.7732 (mt0) cc_final: 0.7488 (mp10) REVERT: B 243 GLU cc_start: 0.7547 (tp30) cc_final: 0.7301 (tp30) REVERT: B 404 GLN cc_start: 0.7985 (tp40) cc_final: 0.7542 (tm-30) REVERT: C 87 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: C 252 MET cc_start: 0.8789 (ttt) cc_final: 0.8389 (ttm) REVERT: D 46 MET cc_start: 0.8180 (mmm) cc_final: 0.7775 (mmm) REVERT: E 39 ASN cc_start: 0.8600 (t0) cc_final: 0.8035 (t0) REVERT: E 52 LEU cc_start: 0.9403 (mt) cc_final: 0.9106 (mt) REVERT: E 64 LEU cc_start: 0.9686 (mt) cc_final: 0.9262 (pp) REVERT: F 7 HIS cc_start: 0.7108 (t-90) cc_final: 0.5373 (m-70) outliers start: 39 outliers final: 35 residues processed: 226 average time/residue: 0.2467 time to fit residues: 82.0014 Evaluate side-chains 228 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 9.9990 chunk 141 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN B 375 GLN C 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 13239 Z= 0.610 Angle : 0.823 12.214 17979 Z= 0.424 Chirality : 0.051 0.220 2085 Planarity : 0.005 0.057 2256 Dihedral : 6.288 59.749 1845 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.29 % Allowed : 16.31 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1677 helix: 0.81 (0.25), residues: 400 sheet: -0.93 (0.23), residues: 460 loop : -1.14 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP E 35 HIS 0.012 0.002 HIS B 146 PHE 0.021 0.003 PHE B 449 TYR 0.032 0.003 TYR A 304 ARG 0.008 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: A 67 ASP cc_start: 0.8549 (m-30) cc_final: 0.8308 (t0) REVERT: A 251 LYS cc_start: 0.8614 (mttt) cc_final: 0.8409 (tptt) REVERT: A 367 ASN cc_start: 0.8294 (p0) cc_final: 0.8073 (p0) REVERT: A 448 LEU cc_start: 0.9087 (tp) cc_final: 0.8828 (tp) REVERT: A 471 MET cc_start: 0.6310 (mmt) cc_final: 0.5526 (mmt) REVERT: B 243 GLU cc_start: 0.7645 (tp30) cc_final: 0.7340 (tp30) REVERT: B 404 GLN cc_start: 0.8047 (tp40) cc_final: 0.7616 (tm-30) REVERT: C 87 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: E 40 ARG cc_start: 0.6993 (ptp-170) cc_final: 0.6669 (ptp-170) REVERT: E 52 LEU cc_start: 0.9449 (mt) cc_final: 0.9143 (mt) REVERT: E 64 LEU cc_start: 0.9697 (mt) cc_final: 0.9270 (pp) REVERT: F 7 HIS cc_start: 0.7057 (t-90) cc_final: 0.5363 (m-70) REVERT: F 51 TRP cc_start: 0.9074 (t60) cc_final: 0.8874 (t-100) outliers start: 46 outliers final: 37 residues processed: 214 average time/residue: 0.2296 time to fit residues: 72.6930 Evaluate side-chains 213 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.0070 chunk 141 optimal weight: 40.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13239 Z= 0.183 Angle : 0.676 15.043 17979 Z= 0.339 Chirality : 0.045 0.304 2085 Planarity : 0.004 0.071 2256 Dihedral : 5.668 46.847 1845 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.79 % Allowed : 18.38 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1677 helix: 0.96 (0.26), residues: 400 sheet: -0.66 (0.23), residues: 469 loop : -0.80 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP E 35 HIS 0.005 0.001 HIS B 86 PHE 0.013 0.001 PHE B 454 TYR 0.033 0.001 TYR A 304 ARG 0.007 0.001 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8449 (m-30) cc_final: 0.8244 (t0) REVERT: A 319 THR cc_start: 0.9196 (m) cc_final: 0.8917 (p) REVERT: A 448 LEU cc_start: 0.9138 (tp) cc_final: 0.8922 (tp) REVERT: A 471 MET cc_start: 0.5585 (mmt) cc_final: 0.5028 (mmt) REVERT: B 243 GLU cc_start: 0.7425 (tp30) cc_final: 0.7181 (tp30) REVERT: B 404 GLN cc_start: 0.7942 (tp40) cc_final: 0.7505 (tm-30) REVERT: C 8 ASN cc_start: 0.8511 (t0) cc_final: 0.7757 (t0) REVERT: C 87 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: C 252 MET cc_start: 0.8778 (ttt) cc_final: 0.8339 (ttm) REVERT: D 46 MET cc_start: 0.8151 (mmm) cc_final: 0.7756 (mmm) REVERT: E 40 ARG cc_start: 0.6912 (ptp-170) cc_final: 0.6622 (ptp-170) REVERT: E 52 LEU cc_start: 0.9367 (mt) cc_final: 0.9062 (mt) REVERT: F 7 HIS cc_start: 0.7112 (t-90) cc_final: 0.5367 (m-70) REVERT: F 51 TRP cc_start: 0.9068 (t60) cc_final: 0.8862 (t-100) outliers start: 25 outliers final: 23 residues processed: 219 average time/residue: 0.2449 time to fit residues: 78.2298 Evaluate side-chains 215 residues out of total 1398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 233 GLN C 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113560 restraints weight = 22032.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117207 restraints weight = 11224.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.119493 restraints weight = 7364.523| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13239 Z= 0.184 Angle : 0.666 15.187 17979 Z= 0.330 Chirality : 0.044 0.341 2085 Planarity : 0.004 0.076 2256 Dihedral : 5.224 40.913 1845 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.07 % Allowed : 18.38 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1677 helix: 1.20 (0.26), residues: 397 sheet: -0.54 (0.23), residues: 474 loop : -0.66 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP E 35 HIS 0.004 0.001 HIS B 5 PHE 0.014 0.001 PHE B 449 TYR 0.029 0.001 TYR A 304 ARG 0.007 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2595.76 seconds wall clock time: 47 minutes 15.70 seconds (2835.70 seconds total)