Starting phenix.real_space_refine on Thu Jul 31 01:26:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_18614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_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/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_18614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_18614.map" model { file = "/net/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_18614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrh_18614/07_2025/8qrh_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.12, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 500 " - " ASN A 154 " " NAG B 500 " - " ASN B 154 " " NAG C 500 " - " ASN C 154 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.8 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: 1.74 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: 4.47 Time building geometry restraints manager: 4.02 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: 0.00 - 1.53: 17086 1.53 - 3.06: 774 3.06 - 4.60: 95 4.60 - 6.13: 21 6.13 - 7.66: 3 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: 0.04 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: 3.070 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 34.120 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- 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 13260 Z= 0.149 Angle : 0.722 7.661 18024 Z= 0.423 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 3) link_NAG-ASN : angle 2.93828 ( 9) hydrogen bonds : bond 0.13053 ( 589) hydrogen bonds : angle 7.57219 ( 1605) SS BOND : bond 0.00462 ( 18) SS BOND : angle 1.29485 ( 36) covalent geometry : bond 0.00274 (13239) covalent geometry : angle 0.71761 (17979) *********************** 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 to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.408 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: 0.2736 time to fit residues: 123.1257 Evaluate side-chains 200 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113156 restraints weight = 22258.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116652 restraints weight = 11339.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118934 restraints weight = 7487.433| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 13260 Z= 0.206 Angle : 0.692 9.082 18024 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 3) link_NAG-ASN : angle 1.58274 ( 9) hydrogen bonds : bond 0.04507 ( 589) hydrogen bonds : angle 6.06701 ( 1605) SS BOND : bond 0.00466 ( 18) SS BOND : angle 0.81248 ( 36) covalent geometry : bond 0.00460 (13239) covalent geometry : angle 0.69134 (17979) *********************** 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 to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8649 (mtpp) REVERT: A 251 LYS cc_start: 0.8580 (mttt) cc_final: 0.8359 (tptt) REVERT: A 394 GLN cc_start: 0.8576 (tp40) cc_final: 0.8308 (tp40) REVERT: B 87 GLN cc_start: 0.7260 (mt0) cc_final: 0.6956 (mp10) REVERT: B 404 GLN cc_start: 0.7952 (tp40) cc_final: 0.7457 (tm-30) REVERT: B 478 MET cc_start: 0.8612 (mpp) cc_final: 0.8326 (ppp) REVERT: C 87 GLN cc_start: 0.7138 (mt0) cc_final: 0.6870 (mp10) REVERT: C 367 ASN cc_start: 0.8072 (t0) cc_final: 0.7851 (t0) REVERT: C 374 MET cc_start: 0.7994 (mtp) cc_final: 0.7787 (mtp) REVERT: E 39 ASN cc_start: 0.7928 (t0) cc_final: 0.7188 (t0) REVERT: E 46 MET cc_start: 0.8319 (ptm) cc_final: 0.8097 (ptt) REVERT: E 48 THR cc_start: 0.9260 (p) cc_final: 0.8960 (t) REVERT: E 52 LEU cc_start: 0.9431 (mt) cc_final: 0.9040 (mt) REVERT: F 7 HIS cc_start: 0.7450 (t-90) cc_final: 0.5312 (m-70) outliers start: 17 outliers final: 12 residues processed: 241 average time/residue: 0.2497 time to fit residues: 87.7423 Evaluate side-chains 208 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 57 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 115 optimal weight: 0.2980 chunk 88 optimal weight: 8.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111891 restraints weight = 22358.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115530 restraints weight = 11378.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117591 restraints weight = 7410.048| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13260 Z= 0.212 Angle : 0.662 9.376 18024 Z= 0.349 Chirality : 0.046 0.170 2085 Planarity : 0.004 0.044 2256 Dihedral : 6.148 48.946 1845 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.65 % Allowed : 11.37 % Favored : 86.98 % 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: -0.04 (0.20), residues: 1677 helix: 1.16 (0.25), residues: 388 sheet: -0.33 (0.24), residues: 467 loop : -0.32 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 35 HIS 0.007 0.001 HIS C 229 PHE 0.022 0.002 PHE B 454 TYR 0.042 0.002 TYR A 304 ARG 0.005 0.001 ARG B 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 3) link_NAG-ASN : angle 1.46385 ( 9) hydrogen bonds : bond 0.04285 ( 589) hydrogen bonds : angle 5.79573 ( 1605) SS BOND : bond 0.00425 ( 18) SS BOND : angle 0.78145 ( 36) covalent geometry : bond 0.00482 (13239) covalent geometry : angle 0.66106 (17979) *********************** 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 231 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.4881 (mmt) cc_final: 0.4381 (mmp) REVERT: B 87 GLN cc_start: 0.7324 (mt0) cc_final: 0.7030 (mp10) REVERT: B 367 ASN cc_start: 0.7784 (p0) cc_final: 0.7578 (p0) REVERT: B 404 GLN cc_start: 0.8016 (tp40) cc_final: 0.7496 (tm-30) REVERT: C 86 HIS cc_start: 0.7811 (m-70) cc_final: 0.7537 (m-70) REVERT: C 252 MET cc_start: 0.8743 (ttt) cc_final: 0.8453 (ttm) REVERT: C 367 ASN cc_start: 0.8041 (t0) cc_final: 0.7742 (t0) REVERT: D 46 MET cc_start: 0.7907 (mmm) cc_final: 0.7321 (mmm) REVERT: E 35 TRP cc_start: 0.8493 (t-100) cc_final: 0.8179 (t-100) REVERT: E 39 ASN cc_start: 0.8341 (t0) cc_final: 0.7641 (t0) REVERT: E 40 ARG cc_start: 0.6318 (ptp-170) cc_final: 0.5728 (ptp-170) REVERT: E 52 LEU cc_start: 0.9426 (mt) cc_final: 0.9118 (mt) REVERT: E 64 LEU cc_start: 0.9691 (mt) cc_final: 0.9241 (pp) REVERT: F 7 HIS cc_start: 0.7473 (t-90) cc_final: 0.5315 (m-70) outliers start: 23 outliers final: 17 residues processed: 218 average time/residue: 0.2295 time to fit residues: 73.1049 Evaluate side-chains 206 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 208 HIS B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111860 restraints weight = 22193.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115387 restraints weight = 11591.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117550 restraints weight = 7700.448| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13260 Z= 0.181 Angle : 0.623 9.595 18024 Z= 0.328 Chirality : 0.044 0.163 2085 Planarity : 0.004 0.042 2256 Dihedral : 5.927 48.639 1845 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.15 % Allowed : 12.66 % Favored : 85.19 % 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: -0.12 (0.20), residues: 1677 helix: 1.11 (0.25), residues: 399 sheet: -0.30 (0.23), residues: 469 loop : -0.45 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 101 HIS 0.006 0.001 HIS A 282 PHE 0.015 0.002 PHE B 332 TYR 0.030 0.002 TYR A 304 ARG 0.004 0.000 ARG A 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 3) link_NAG-ASN : angle 1.39369 ( 9) hydrogen bonds : bond 0.04018 ( 589) hydrogen bonds : angle 5.64632 ( 1605) SS BOND : bond 0.00494 ( 18) SS BOND : angle 0.84686 ( 36) covalent geometry : bond 0.00416 (13239) covalent geometry : angle 0.62219 (17979) *********************** 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 235 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.7534 (mt) cc_final: 0.6602 (tt) REVERT: B 367 ASN cc_start: 0.7762 (p0) cc_final: 0.7541 (p0) REVERT: B 404 GLN cc_start: 0.7852 (tp40) cc_final: 0.7356 (tm-30) REVERT: C 86 HIS cc_start: 0.7836 (m-70) cc_final: 0.7510 (m-70) REVERT: C 252 MET cc_start: 0.8781 (ttt) cc_final: 0.8419 (ttm) REVERT: D 46 MET cc_start: 0.7892 (mmm) cc_final: 0.7272 (mmm) REVERT: E 35 TRP cc_start: 0.8391 (t-100) cc_final: 0.8143 (t-100) REVERT: E 39 ASN cc_start: 0.8721 (t0) cc_final: 0.8321 (t0) REVERT: E 40 ARG cc_start: 0.6467 (ptp-170) cc_final: 0.6037 (ptp-170) REVERT: E 52 LEU cc_start: 0.9410 (mt) cc_final: 0.9106 (mt) REVERT: E 64 LEU cc_start: 0.9678 (mt) cc_final: 0.9256 (pp) REVERT: F 7 HIS cc_start: 0.7468 (t-90) cc_final: 0.5316 (m-70) outliers start: 30 outliers final: 26 residues processed: 224 average time/residue: 0.2475 time to fit residues: 81.3245 Evaluate side-chains 217 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 349 SER Chi-restraints excluded: chain A residue 398 SER 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 140 THR Chi-restraints excluded: chain B residue 257 LEU 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 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 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 84 optimal weight: 0.9980 chunk 142 optimal weight: 40.0000 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.150081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112452 restraints weight = 22329.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116131 restraints weight = 11391.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118316 restraints weight = 7472.940| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13260 Z= 0.132 Angle : 0.600 10.320 18024 Z= 0.310 Chirality : 0.043 0.152 2085 Planarity : 0.004 0.051 2256 Dihedral : 5.625 45.235 1845 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.07 % Allowed : 13.88 % Favored : 84.05 % 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: -0.09 (0.20), residues: 1677 helix: 1.13 (0.25), residues: 405 sheet: -0.26 (0.23), residues: 469 loop : -0.46 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 101 HIS 0.004 0.001 HIS A 282 PHE 0.014 0.001 PHE B 454 TYR 0.029 0.002 TYR A 304 ARG 0.005 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 3) link_NAG-ASN : angle 1.32967 ( 9) hydrogen bonds : bond 0.03831 ( 589) hydrogen bonds : angle 5.52489 ( 1605) SS BOND : bond 0.00328 ( 18) SS BOND : angle 0.66179 ( 36) covalent geometry : bond 0.00293 (13239) covalent geometry : angle 0.59963 (17979) *********************** 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 to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.7542 (mt) cc_final: 0.6601 (tt) REVERT: B 87 GLN cc_start: 0.7561 (mt0) cc_final: 0.7264 (mp10) REVERT: B 367 ASN cc_start: 0.7736 (p0) cc_final: 0.7528 (p0) REVERT: B 404 GLN cc_start: 0.7894 (tp40) cc_final: 0.7422 (tm-30) REVERT: C 8 ASN cc_start: 0.8460 (t0) cc_final: 0.7664 (t0) REVERT: C 86 HIS cc_start: 0.7829 (m-70) cc_final: 0.7545 (m-70) REVERT: C 87 GLN cc_start: 0.7083 (mp10) cc_final: 0.6813 (mp10) REVERT: C 196 GLN cc_start: 0.8570 (mm110) cc_final: 0.8349 (mm-40) REVERT: C 252 MET cc_start: 0.8731 (ttt) cc_final: 0.8461 (ttm) REVERT: D 46 MET cc_start: 0.7871 (mmm) cc_final: 0.7418 (mmm) REVERT: E 35 TRP cc_start: 0.8377 (t-100) cc_final: 0.8137 (t-100) REVERT: E 39 ASN cc_start: 0.8658 (t0) cc_final: 0.8202 (t0) REVERT: E 40 ARG cc_start: 0.6582 (ptp-170) cc_final: 0.6124 (ptp-170) REVERT: E 52 LEU cc_start: 0.9368 (mt) cc_final: 0.9062 (mt) REVERT: E 64 LEU cc_start: 0.9671 (mt) cc_final: 0.9223 (pp) REVERT: F 7 HIS cc_start: 0.7453 (t-90) cc_final: 0.5314 (m-70) outliers start: 29 outliers final: 22 residues processed: 223 average time/residue: 0.2362 time to fit residues: 77.9615 Evaluate side-chains 214 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.418 ------------------------------------------------------------------------------- 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 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 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 C residue 190 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 163 optimal weight: 40.0000 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** C 87 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 = 0.3867 r_free = 0.3867 target = 0.148787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111097 restraints weight = 22539.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114727 restraints weight = 11485.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117026 restraints weight = 7520.955| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13260 Z= 0.177 Angle : 0.617 10.291 18024 Z= 0.319 Chirality : 0.044 0.154 2085 Planarity : 0.004 0.055 2256 Dihedral : 5.582 48.074 1845 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.65 % Allowed : 14.23 % Favored : 83.12 % 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: 1.13 (0.25), residues: 405 sheet: -0.38 (0.24), residues: 467 loop : -0.58 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 51 HIS 0.006 0.001 HIS A 282 PHE 0.015 0.002 PHE B 454 TYR 0.029 0.002 TYR A 304 ARG 0.006 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 3) link_NAG-ASN : angle 1.30386 ( 9) hydrogen bonds : bond 0.03876 ( 589) hydrogen bonds : angle 5.48565 ( 1605) SS BOND : bond 0.00396 ( 18) SS BOND : angle 0.61328 ( 36) covalent geometry : bond 0.00407 (13239) covalent geometry : angle 0.61653 (17979) *********************** 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 235 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.7436 (mt) cc_final: 0.6461 (tt) REVERT: B 87 GLN cc_start: 0.7608 (mt0) cc_final: 0.7372 (mp10) REVERT: B 404 GLN cc_start: 0.7857 (tp40) cc_final: 0.7391 (tm-30) REVERT: C 8 ASN cc_start: 0.8471 (t0) cc_final: 0.7487 (t0) REVERT: C 86 HIS cc_start: 0.7826 (m-70) cc_final: 0.7581 (m-70) REVERT: C 87 GLN cc_start: 0.7202 (mp10) cc_final: 0.6831 (mp10) REVERT: C 196 GLN cc_start: 0.8630 (mm110) cc_final: 0.8341 (mm-40) REVERT: C 252 MET cc_start: 0.8748 (ttt) cc_final: 0.8435 (ttm) REVERT: D 46 MET cc_start: 0.7940 (mmm) cc_final: 0.7491 (mmm) REVERT: E 39 ASN cc_start: 0.8571 (t0) cc_final: 0.8032 (t0) REVERT: E 40 ARG cc_start: 0.6602 (ptp-170) cc_final: 0.6254 (ptp-170) REVERT: E 52 LEU cc_start: 0.9323 (mt) cc_final: 0.9014 (mt) REVERT: F 7 HIS cc_start: 0.7502 (t-90) cc_final: 0.5347 (m-70) outliers start: 37 outliers final: 28 residues processed: 225 average time/residue: 0.2343 time to fit residues: 77.6790 Evaluate side-chains 219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 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 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 C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 52 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 163 optimal weight: 30.0000 chunk 30 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** C 87 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 = 0.3855 r_free = 0.3855 target = 0.147913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110231 restraints weight = 22239.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113703 restraints weight = 11452.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116011 restraints weight = 7580.149| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13260 Z= 0.211 Angle : 0.660 13.551 18024 Z= 0.338 Chirality : 0.045 0.154 2085 Planarity : 0.004 0.058 2256 Dihedral : 5.666 50.634 1845 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.65 % Allowed : 14.81 % Favored : 82.55 % 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: -0.30 (0.20), residues: 1677 helix: 1.13 (0.26), residues: 401 sheet: -0.47 (0.24), residues: 464 loop : -0.63 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP E 35 HIS 0.006 0.001 HIS A 282 PHE 0.013 0.002 PHE B 332 TYR 0.029 0.002 TYR A 304 ARG 0.010 0.001 ARG F 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 3) link_NAG-ASN : angle 1.35748 ( 9) hydrogen bonds : bond 0.03940 ( 589) hydrogen bonds : angle 5.50710 ( 1605) SS BOND : bond 0.00528 ( 18) SS BOND : angle 0.80135 ( 36) covalent geometry : bond 0.00492 (13239) covalent geometry : angle 0.65890 (17979) *********************** 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 233 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 LEU cc_start: 0.7493 (mt) cc_final: 0.6478 (tt) REVERT: B 87 GLN cc_start: 0.7675 (mt0) cc_final: 0.7364 (mp10) REVERT: B 243 GLU cc_start: 0.7451 (tp30) cc_final: 0.7242 (tp30) REVERT: B 404 GLN cc_start: 0.7942 (tp40) cc_final: 0.7496 (tm-30) REVERT: C 87 GLN cc_start: 0.7351 (mp10) cc_final: 0.6907 (mp10) REVERT: C 196 GLN cc_start: 0.8618 (mm110) cc_final: 0.8213 (mm-40) REVERT: C 252 MET cc_start: 0.8764 (ttt) cc_final: 0.8430 (ttm) REVERT: D 46 MET cc_start: 0.7937 (mmm) cc_final: 0.7486 (mmm) REVERT: E 40 ARG cc_start: 0.6862 (ptp-170) cc_final: 0.6605 (ptp-170) REVERT: E 52 LEU cc_start: 0.9321 (mt) cc_final: 0.9008 (mt) REVERT: F 7 HIS cc_start: 0.7574 (t-90) cc_final: 0.5366 (m-70) outliers start: 37 outliers final: 33 residues processed: 221 average time/residue: 0.2376 time to fit residues: 77.8271 Evaluate side-chains 224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 2 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111043 restraints weight = 22186.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114632 restraints weight = 11340.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116935 restraints weight = 7451.053| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13260 Z= 0.162 Angle : 0.647 13.597 18024 Z= 0.327 Chirality : 0.044 0.189 2085 Planarity : 0.004 0.063 2256 Dihedral : 5.552 48.143 1845 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.58 % Allowed : 15.45 % Favored : 81.97 % 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: -0.26 (0.20), residues: 1677 helix: 1.18 (0.26), residues: 401 sheet: -0.46 (0.24), residues: 467 loop : -0.61 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 35 HIS 0.005 0.001 HIS A 282 PHE 0.015 0.001 PHE B 449 TYR 0.033 0.002 TYR A 304 ARG 0.007 0.000 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 3) link_NAG-ASN : angle 1.32155 ( 9) hydrogen bonds : bond 0.03839 ( 589) hydrogen bonds : angle 5.43765 ( 1605) SS BOND : bond 0.00333 ( 18) SS BOND : angle 0.91823 ( 36) covalent geometry : bond 0.00373 (13239) covalent geometry : angle 0.64610 (17979) *********************** 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 to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.9088 (m) cc_final: 0.8880 (p) REVERT: B 404 GLN cc_start: 0.7916 (tp40) cc_final: 0.7470 (tm-30) REVERT: C 8 ASN cc_start: 0.8478 (t0) cc_final: 0.7603 (t0) REVERT: C 87 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6806 (mp10) REVERT: C 196 GLN cc_start: 0.8587 (mm110) cc_final: 0.8173 (mm-40) REVERT: C 252 MET cc_start: 0.8767 (ttt) cc_final: 0.8381 (ttm) REVERT: D 46 MET cc_start: 0.7920 (mmm) cc_final: 0.7477 (mmm) REVERT: E 40 ARG cc_start: 0.7131 (ptp-170) cc_final: 0.6751 (ptp-170) REVERT: E 52 LEU cc_start: 0.9302 (mt) cc_final: 0.9033 (mt) REVERT: F 7 HIS cc_start: 0.7568 (t-90) cc_final: 0.5353 (m-70) outliers start: 36 outliers final: 32 residues processed: 226 average time/residue: 0.2271 time to fit residues: 76.3370 Evaluate side-chains 224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.386 ------------------------------------------------------------------------------- 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 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 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 171 LYS Chi-restraints excluded: chain B residue 188 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 C residue 347 HIS Chi-restraints excluded: chain D residue 20 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 163 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 34 optimal weight: 0.4980 chunk 72 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 HIS B 366 ASN B 375 GLN C 86 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110204 restraints weight = 22324.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113277 restraints weight = 12895.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115797 restraints weight = 8538.057| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13260 Z= 0.219 Angle : 0.702 16.172 18024 Z= 0.353 Chirality : 0.046 0.252 2085 Planarity : 0.004 0.066 2256 Dihedral : 5.633 50.878 1845 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.43 % Allowed : 15.81 % Favored : 81.76 % 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: -0.41 (0.20), residues: 1677 helix: 1.09 (0.25), residues: 401 sheet: -0.54 (0.24), residues: 462 loop : -0.73 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP E 35 HIS 0.006 0.001 HIS A 282 PHE 0.013 0.002 PHE B 332 TYR 0.034 0.002 TYR A 304 ARG 0.007 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 3) link_NAG-ASN : angle 1.38128 ( 9) hydrogen bonds : bond 0.03975 ( 589) hydrogen bonds : angle 5.47949 ( 1605) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.30262 ( 36) covalent geometry : bond 0.00511 (13239) covalent geometry : angle 0.70009 (17979) *********************** 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 224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 MET cc_start: 0.5736 (mmt) cc_final: 0.4877 (mmt) REVERT: B 243 GLU cc_start: 0.7510 (tp30) cc_final: 0.7252 (tp30) REVERT: B 404 GLN cc_start: 0.8050 (tp40) cc_final: 0.7596 (tm-30) REVERT: C 196 GLN cc_start: 0.8585 (mm110) cc_final: 0.8161 (mm-40) REVERT: C 252 MET cc_start: 0.8783 (ttt) cc_final: 0.8406 (ttm) REVERT: D 46 MET cc_start: 0.7984 (mmm) cc_final: 0.7562 (mmm) REVERT: E 40 ARG cc_start: 0.7147 (ptp-170) cc_final: 0.6692 (ptp-170) REVERT: E 52 LEU cc_start: 0.9406 (mt) cc_final: 0.9110 (mt) REVERT: F 7 HIS cc_start: 0.7454 (t-90) cc_final: 0.5371 (m-70) outliers start: 34 outliers final: 30 residues processed: 214 average time/residue: 0.2280 time to fit residues: 72.5771 Evaluate side-chains 215 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.395 ------------------------------------------------------------------------------- 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 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 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 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 46 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 134 optimal weight: 0.0980 chunk 25 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 86 HIS ** E 39 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.150906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.113799 restraints weight = 22125.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117446 restraints weight = 11152.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119696 restraints weight = 7286.571| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13260 Z= 0.117 Angle : 0.667 16.494 18024 Z= 0.328 Chirality : 0.043 0.186 2085 Planarity : 0.004 0.076 2256 Dihedral : 5.283 42.156 1845 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 17.45 % Favored : 81.26 % 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: 1.28 (0.26), residues: 398 sheet: -0.40 (0.24), residues: 470 loop : -0.59 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP E 35 HIS 0.004 0.001 HIS B 5 PHE 0.014 0.001 PHE B 449 TYR 0.031 0.001 TYR A 304 ARG 0.007 0.000 ARG B 73 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 3) link_NAG-ASN : angle 1.24574 ( 9) hydrogen bonds : bond 0.03746 ( 589) hydrogen bonds : angle 5.30433 ( 1605) SS BOND : bond 0.00271 ( 18) SS BOND : angle 1.08721 ( 36) covalent geometry : bond 0.00253 (13239) covalent geometry : angle 0.66572 (17979) ********************** 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 223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (mtt) REVERT: A 471 MET cc_start: 0.5375 (mmt) cc_final: 0.4672 (mpp) REVERT: B 243 GLU cc_start: 0.7304 (tp30) cc_final: 0.7063 (tp30) REVERT: B 404 GLN cc_start: 0.7888 (tp40) cc_final: 0.7445 (tm-30) REVERT: B 469 LEU cc_start: 0.9239 (tp) cc_final: 0.8983 (pp) REVERT: B 478 MET cc_start: 0.8009 (mpp) cc_final: 0.7393 (ppp) REVERT: C 8 ASN cc_start: 0.8403 (t0) cc_final: 0.7715 (t0) REVERT: C 69 LYS cc_start: 0.8753 (mttm) cc_final: 0.8493 (mttm) REVERT: C 87 GLN cc_start: 0.7360 (mp10) cc_final: 0.6723 (mp10) REVERT: C 196 GLN cc_start: 0.8543 (mm110) cc_final: 0.8146 (mm-40) REVERT: C 252 MET cc_start: 0.8764 (ttt) cc_final: 0.8353 (ttm) REVERT: D 46 MET cc_start: 0.8182 (mmm) cc_final: 0.7743 (mmm) REVERT: E 40 ARG cc_start: 0.7340 (ptp-170) cc_final: 0.6962 (ptp-170) REVERT: E 52 LEU cc_start: 0.9294 (mt) cc_final: 0.8999 (mt) REVERT: F 7 HIS cc_start: 0.7551 (t-90) cc_final: 0.5339 (m-70) outliers start: 18 outliers final: 15 residues processed: 217 average time/residue: 0.2395 time to fit residues: 76.7272 Evaluate side-chains 208 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain B residue 56 THR 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 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 330 VAL 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 31 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 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 375 GLN C 233 GLN ** E 39 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.147316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109879 restraints weight = 22120.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113386 restraints weight = 11443.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115616 restraints weight = 7566.832| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13260 Z= 0.268 Angle : 0.746 17.334 18024 Z= 0.375 Chirality : 0.047 0.217 2085 Planarity : 0.004 0.068 2256 Dihedral : 5.615 51.717 1845 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.07 % Allowed : 16.95 % Favored : 80.97 % 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: -0.41 (0.20), residues: 1677 helix: 1.26 (0.26), residues: 398 sheet: -0.64 (0.24), residues: 462 loop : -0.74 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP E 35 HIS 0.007 0.001 HIS A 282 PHE 0.015 0.002 PHE B 108 TYR 0.033 0.002 TYR A 304 ARG 0.007 0.001 ARG A 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 3) link_NAG-ASN : angle 1.48105 ( 9) hydrogen bonds : bond 0.04040 ( 589) hydrogen bonds : angle 5.47795 ( 1605) SS BOND : bond 0.00521 ( 18) SS BOND : angle 1.29558 ( 36) covalent geometry : bond 0.00626 (13239) covalent geometry : angle 0.74371 (17979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4319.92 seconds wall clock time: 76 minutes 35.16 seconds (4595.16 seconds total)