Starting phenix.real_space_refine on Fri Feb 6 04:35:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw5_48677/02_2026/9mw5_48677.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 81 5.16 5 Na 6 4.78 5 C 10752 2.51 5 N 2985 2.21 5 O 8744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22568 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4723 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 557} Chain breaks: 1 Chain: "B" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4723 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 557} Chain breaks: 1 Chain: "C" Number of atoms: 4723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4723 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 557} Chain breaks: 1 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 1078 Classifications: {'water': 1078} Link IDs: {None: 1077} Chain: "B" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 1077 Classifications: {'water': 1077} Link IDs: {None: 1076} Chain: "C" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 1101 Classifications: {'water': 1101} Link IDs: {None: 1100} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 745 Classifications: {'water': 745} Link IDs: {None: 744} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 757 Classifications: {'water': 757} Link IDs: {None: 756} Chain: "F" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 758 Classifications: {'water': 758} Link IDs: {None: 757} Time building chain proxies: 5.76, per 1000 atoms: 0.26 Number of scatterers: 22568 At special positions: 0 Unit cell: (139.239, 148.716, 178.605, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 Na 6 11.00 O 8744 8.00 N 2985 7.00 C 10752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 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 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 876.1 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3972 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 44 sheets defined 20.8% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.998A pdb=" N ARG A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 501 through 546 removed outlier: 4.438A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.972A pdb=" N ARG B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 501 through 546 removed outlier: 4.406A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 701 through 710 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 358 through 363 removed outlier: 3.703A pdb=" N ALA C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 459 through 461 No H-bonds generated for 'chain 'C' and resid 459 through 461' Processing helix chain 'C' and resid 501 through 546 removed outlier: 4.382A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 690 through 697 Processing helix chain 'C' and resid 701 through 710 Processing helix chain 'C' and resid 712 through 717 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.506A pdb=" N GLU D 111 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'F' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 562 removed outlier: 6.778A pdb=" N VAL A 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 667 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN A 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.535A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.535A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 191 removed outlier: 3.782A pdb=" N TYR A 179 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN A 172 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 185 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL A 170 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU A 187 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 168 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A 189 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS A 166 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR A 164 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 262 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 3.849A pdb=" N PHE A 262 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG A 342 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP A 323 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU A 344 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN A 321 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 346 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N PHE A 319 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB2, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB3, first strand: chain 'A' and resid 638 through 643 removed outlier: 5.627A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 665 through 667 removed outlier: 3.854A pdb=" N THR A 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.656A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.549A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 366 through 372 removed outlier: 6.549A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 179 through 191 removed outlier: 3.778A pdb=" N TYR B 179 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN B 172 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 185 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 170 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU B 187 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 168 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG B 189 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS B 166 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N TYR B 164 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 262 " --> pdb=" O PHE B 175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 235 through 236 removed outlier: 3.832A pdb=" N PHE B 262 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 324 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC2, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC3, first strand: chain 'B' and resid 375 through 380 Processing sheet with id=AC4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 643 removed outlier: 5.653A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 665 through 667 removed outlier: 3.842A pdb=" N THR B 665 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.580A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.546A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 366 through 372 removed outlier: 6.546A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 180 through 191 removed outlier: 5.523A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE C 262 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 235 through 236 removed outlier: 3.849A pdb=" N PHE C 262 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 342 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP C 323 " --> pdb=" O ARG C 342 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 344 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN C 321 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR C 346 " --> pdb=" O PHE C 319 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE C 319 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD4, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD5, first strand: chain 'C' and resid 375 through 380 Processing sheet with id=AD6, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD7, first strand: chain 'C' and resid 638 through 643 removed outlier: 5.586A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.339A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.339A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AE4, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.366A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.366A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.136A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.136A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 94 " --> pdb=" O THR F 119 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2181 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: 6.16 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5655 1.34 - 1.46: 4254 1.46 - 1.58: 7428 1.58 - 1.70: 0 1.70 - 1.81: 126 Bond restraints: 17463 Sorted by residual: bond pdb=" C ALA C 444 " pdb=" N THR C 445 " ideal model delta sigma weight residual 1.331 1.250 0.081 1.33e-02 5.65e+03 3.68e+01 bond pdb=" C THR C 445 " pdb=" N GLY C 446 " ideal model delta sigma weight residual 1.332 1.233 0.099 1.66e-02 3.63e+03 3.56e+01 bond pdb=" CA ALA C 444 " pdb=" CB ALA C 444 " ideal model delta sigma weight residual 1.531 1.496 0.035 1.58e-02 4.01e+03 4.91e+00 bond pdb=" CE LYS A 238 " pdb=" NZ LYS A 238 " ideal model delta sigma weight residual 1.489 1.553 -0.064 3.00e-02 1.11e+03 4.52e+00 bond pdb=" N ALA C 444 " pdb=" CA ALA C 444 " ideal model delta sigma weight residual 1.454 1.479 -0.024 1.15e-02 7.56e+03 4.43e+00 ... (remaining 17458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 23565 2.58 - 5.15: 136 5.15 - 7.73: 6 7.73 - 10.31: 1 10.31 - 12.89: 1 Bond angle restraints: 23709 Sorted by residual: angle pdb=" C ALA C 444 " pdb=" N THR C 445 " pdb=" CA THR C 445 " ideal model delta sigma weight residual 121.05 133.94 -12.89 1.43e+00 4.89e-01 8.12e+01 angle pdb=" CA ALA C 444 " pdb=" C ALA C 444 " pdb=" N THR C 445 " ideal model delta sigma weight residual 115.23 122.86 -7.63 1.30e+00 5.92e-01 3.44e+01 angle pdb=" CA THR C 445 " pdb=" C THR C 445 " pdb=" N GLY C 446 " ideal model delta sigma weight residual 115.91 122.66 -6.75 1.29e+00 6.01e-01 2.74e+01 angle pdb=" O ALA C 444 " pdb=" C ALA C 444 " pdb=" N THR C 445 " ideal model delta sigma weight residual 123.03 117.75 5.28 1.13e+00 7.83e-01 2.18e+01 angle pdb=" O THR C 445 " pdb=" C THR C 445 " pdb=" N GLY C 446 " ideal model delta sigma weight residual 123.06 117.97 5.09 1.20e+00 6.94e-01 1.80e+01 ... (remaining 23704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 9455 17.60 - 35.21: 692 35.21 - 52.81: 125 52.81 - 70.42: 48 70.42 - 88.02: 33 Dihedral angle restraints: 10353 sinusoidal: 4140 harmonic: 6213 Sorted by residual: dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS C 271 " pdb=" CB CYS C 271 " ideal model delta sinusoidal sigma weight residual -86.00 -42.89 -43.11 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS A 207 " pdb=" SG CYS A 207 " pdb=" SG CYS A 271 " pdb=" CB CYS A 271 " ideal model delta sinusoidal sigma weight residual -86.00 -43.94 -42.06 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS B 271 " pdb=" CB CYS B 271 " ideal model delta sinusoidal sigma weight residual -86.00 -47.23 -38.77 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 10350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1472 0.029 - 0.057: 714 0.057 - 0.086: 197 0.086 - 0.114: 142 0.114 - 0.143: 31 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA VAL C 259 " pdb=" N VAL C 259 " pdb=" C VAL C 259 " pdb=" CB VAL C 259 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE B 146 " pdb=" N ILE B 146 " pdb=" C ILE B 146 " pdb=" CB ILE B 146 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 146 " pdb=" N ILE A 146 " pdb=" C ILE A 146 " pdb=" CB ILE A 146 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 2553 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 523 " 0.524 9.50e-02 1.11e+02 2.35e-01 3.45e+01 pdb=" NE ARG A 523 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 523 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 523 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 523 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 523 " 0.404 9.50e-02 1.11e+02 1.81e-01 2.08e+01 pdb=" NE ARG B 523 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 523 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 523 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 523 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 427 " 0.381 9.50e-02 1.11e+02 1.71e-01 1.84e+01 pdb=" NE ARG C 427 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 427 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 427 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 427 " 0.009 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7527 2.87 - 3.38: 27961 3.38 - 3.88: 43589 3.88 - 4.39: 51557 4.39 - 4.90: 78169 Nonbonded interactions: 208803 Sorted by model distance: nonbonded pdb="NA NA A 802 " pdb=" O HOH A1016 " model vdw 2.359 2.470 nonbonded pdb="NA NA B 801 " pdb=" O HOH B1076 " model vdw 2.392 2.470 nonbonded pdb="NA NA C 801 " pdb=" O HOH C1060 " model vdw 2.451 2.470 nonbonded pdb=" OD1 ASN B 540 " pdb="NA NA B 802 " model vdw 2.505 2.470 nonbonded pdb=" NZ LYS B 238 " pdb=" O ALA C 717 " model vdw 2.512 3.120 ... (remaining 208798 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.410 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 0.099 17475 Z= 0.141 Angle : 0.553 12.886 23733 Z= 0.311 Chirality : 0.041 0.143 2556 Planarity : 0.008 0.235 3087 Dihedral : 14.049 88.019 6345 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2112 helix: 0.76 (0.29), residues: 315 sheet: -0.16 (0.18), residues: 729 loop : 0.42 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 523 TYR 0.017 0.001 TYR B 640 PHE 0.014 0.001 PHE B 300 TRP 0.014 0.001 TRP C 356 HIS 0.024 0.002 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00276 (17463) covalent geometry : angle 0.55272 (23709) SS BOND : bond 0.00239 ( 12) SS BOND : angle 0.63039 ( 24) hydrogen bonds : bond 0.09400 ( 695) hydrogen bonds : angle 7.14549 ( 2181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.884 Fit side-chains REVERT: A 132 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7624 (tpm170) REVERT: A 199 ASP cc_start: 0.8945 (m-30) cc_final: 0.8660 (m-30) REVERT: A 308 HIS cc_start: 0.8573 (p-80) cc_final: 0.8329 (p-80) REVERT: B 132 ARG cc_start: 0.8429 (tpp80) cc_final: 0.7729 (tpm170) REVERT: B 308 HIS cc_start: 0.8520 (p-80) cc_final: 0.8224 (p90) REVERT: B 494 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7736 (mtm180) REVERT: C 132 ARG cc_start: 0.8477 (tpp80) cc_final: 0.7789 (tpt170) REVERT: D 83 MET cc_start: 0.5389 (mtp) cc_final: 0.4692 (mtp) REVERT: E 83 MET cc_start: 0.5303 (mtp) cc_final: 0.4880 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.8474 time to fit residues: 230.5555 Evaluate side-chains 211 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 141 ASN A 657 HIS A 692 HIS B 112 GLN B 141 ASN B 657 HIS B 674 ASN C 141 ASN C 308 HIS C 580 ASN C 657 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.178155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109706 restraints weight = 19234.011| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.45 r_work: 0.3129 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17475 Z= 0.208 Angle : 0.577 4.900 23733 Z= 0.323 Chirality : 0.044 0.156 2556 Planarity : 0.006 0.057 3087 Dihedral : 4.984 19.099 2406 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.93 % Allowed : 4.50 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2112 helix: 1.17 (0.29), residues: 324 sheet: 0.06 (0.18), residues: 720 loop : 0.26 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 523 TYR 0.016 0.002 TYR B 296 PHE 0.023 0.002 PHE B 287 TRP 0.016 0.002 TRP C 356 HIS 0.009 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00441 (17463) covalent geometry : angle 0.57664 (23709) SS BOND : bond 0.00633 ( 12) SS BOND : angle 0.76067 ( 24) hydrogen bonds : bond 0.05490 ( 695) hydrogen bonds : angle 6.08474 ( 2181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.871 Fit side-chains REVERT: A 132 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7396 (tpm170) REVERT: A 308 HIS cc_start: 0.8471 (p-80) cc_final: 0.8226 (p90) REVERT: A 657 HIS cc_start: 0.7215 (t70) cc_final: 0.6959 (t-90) REVERT: B 132 ARG cc_start: 0.8373 (tpp80) cc_final: 0.7483 (tpm170) REVERT: B 308 HIS cc_start: 0.8457 (p-80) cc_final: 0.8157 (p90) REVERT: B 434 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 496 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8469 (mmpt) REVERT: B 679 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: C 132 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7435 (tpm170) REVERT: C 624 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8039 (mtp-110) REVERT: D 83 MET cc_start: 0.5490 (mtp) cc_final: 0.4978 (mtp) REVERT: E 83 MET cc_start: 0.5250 (mtp) cc_final: 0.4981 (mtp) outliers start: 17 outliers final: 11 residues processed: 218 average time/residue: 0.8235 time to fit residues: 200.7532 Evaluate side-chains 217 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.176157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107821 restraints weight = 19255.743| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.45 r_work: 0.3104 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17475 Z= 0.264 Angle : 0.621 6.059 23733 Z= 0.348 Chirality : 0.046 0.149 2556 Planarity : 0.006 0.052 3087 Dihedral : 5.276 19.970 2406 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.37 % Allowed : 5.48 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2112 helix: 1.23 (0.29), residues: 324 sheet: 0.05 (0.18), residues: 720 loop : 0.30 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 136 TYR 0.017 0.002 TYR B 142 PHE 0.026 0.002 PHE A 287 TRP 0.017 0.003 TRP C 356 HIS 0.009 0.002 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00567 (17463) covalent geometry : angle 0.62075 (23709) SS BOND : bond 0.00928 ( 12) SS BOND : angle 0.89060 ( 24) hydrogen bonds : bond 0.05854 ( 695) hydrogen bonds : angle 6.17978 ( 2181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.836 Fit side-chains REVERT: A 132 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7432 (tpm170) REVERT: A 199 ASP cc_start: 0.8940 (m-30) cc_final: 0.8676 (m-30) REVERT: A 308 HIS cc_start: 0.8459 (p-80) cc_final: 0.8220 (p90) REVERT: B 132 ARG cc_start: 0.8378 (tpp80) cc_final: 0.7473 (tpm170) REVERT: B 308 HIS cc_start: 0.8471 (p-80) cc_final: 0.8173 (p90) REVERT: B 434 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 496 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8454 (mmpt) REVERT: B 679 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: C 132 ARG cc_start: 0.8427 (tpp80) cc_final: 0.7456 (tpm170) REVERT: C 624 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7985 (mtp-110) REVERT: F 102 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7284 (pttp) outliers start: 25 outliers final: 12 residues processed: 221 average time/residue: 0.7858 time to fit residues: 195.3167 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 141 ASN C 308 HIS C 657 HIS F 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108524 restraints weight = 19319.967| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.45 r_work: 0.3117 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17475 Z= 0.203 Angle : 0.560 5.114 23733 Z= 0.315 Chirality : 0.044 0.148 2556 Planarity : 0.005 0.039 3087 Dihedral : 5.116 20.137 2406 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.43 % Allowed : 6.41 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2112 helix: 1.33 (0.29), residues: 324 sheet: 0.03 (0.18), residues: 720 loop : 0.32 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.016 0.002 TYR B 441 PHE 0.023 0.002 PHE A 287 TRP 0.016 0.002 TRP A 539 HIS 0.008 0.002 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00429 (17463) covalent geometry : angle 0.56002 (23709) SS BOND : bond 0.00655 ( 12) SS BOND : angle 0.71964 ( 24) hydrogen bonds : bond 0.05366 ( 695) hydrogen bonds : angle 6.01024 ( 2181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.882 Fit side-chains REVERT: A 132 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7394 (tpm170) REVERT: A 199 ASP cc_start: 0.8960 (m-30) cc_final: 0.8709 (m-30) REVERT: A 219 GLU cc_start: 0.8733 (tt0) cc_final: 0.8527 (tt0) REVERT: A 308 HIS cc_start: 0.8466 (p-80) cc_final: 0.8233 (p90) REVERT: A 658 GLN cc_start: 0.8004 (pm20) cc_final: 0.7610 (pm20) REVERT: B 132 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7457 (tpm170) REVERT: B 308 HIS cc_start: 0.8488 (p-80) cc_final: 0.8179 (p90) REVERT: B 434 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8295 (pp) REVERT: B 496 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8483 (mmpt) REVERT: B 502 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: B 679 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: B 695 LYS cc_start: 0.8190 (tptt) cc_final: 0.7022 (ptpt) REVERT: C 132 ARG cc_start: 0.8416 (tpp80) cc_final: 0.7451 (tpm170) REVERT: D 102 LYS cc_start: 0.7938 (pttp) cc_final: 0.7561 (pttm) REVERT: F 102 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7205 (pttp) outliers start: 26 outliers final: 12 residues processed: 224 average time/residue: 0.7258 time to fit residues: 182.9282 Evaluate side-chains 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 203 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111862 restraints weight = 19167.545| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.41 r_work: 0.3165 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17475 Z= 0.173 Angle : 0.530 4.616 23733 Z= 0.299 Chirality : 0.043 0.147 2556 Planarity : 0.004 0.039 3087 Dihedral : 4.998 20.239 2406 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.54 % Allowed : 7.02 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2112 helix: 1.41 (0.29), residues: 324 sheet: 0.04 (0.18), residues: 720 loop : 0.36 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 136 TYR 0.015 0.002 TYR B 441 PHE 0.021 0.002 PHE A 287 TRP 0.015 0.002 TRP A 539 HIS 0.007 0.002 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00362 (17463) covalent geometry : angle 0.52974 (23709) SS BOND : bond 0.00551 ( 12) SS BOND : angle 0.67910 ( 24) hydrogen bonds : bond 0.05099 ( 695) hydrogen bonds : angle 5.88941 ( 2181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.828 Fit side-chains REVERT: A 132 ARG cc_start: 0.8388 (tpp80) cc_final: 0.7526 (tpm170) REVERT: A 199 ASP cc_start: 0.8942 (m-30) cc_final: 0.8692 (m-30) REVERT: A 308 HIS cc_start: 0.8515 (p-80) cc_final: 0.8289 (p90) REVERT: A 658 GLN cc_start: 0.8045 (pm20) cc_final: 0.7729 (pm20) REVERT: B 132 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7582 (tpm170) REVERT: B 308 HIS cc_start: 0.8553 (p-80) cc_final: 0.8247 (p90) REVERT: B 434 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8365 (pp) REVERT: B 496 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8595 (mmpt) REVERT: B 679 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: B 695 LYS cc_start: 0.8305 (tptt) cc_final: 0.7220 (ptpt) REVERT: C 132 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7576 (tpm170) REVERT: C 320 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8663 (tttm) REVERT: F 102 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7290 (pttp) outliers start: 28 outliers final: 14 residues processed: 222 average time/residue: 0.7038 time to fit residues: 175.7257 Evaluate side-chains 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 692 HIS B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 141 ASN C 308 HIS C 580 ASN C 657 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110822 restraints weight = 19313.270| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.39 r_work: 0.3151 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17475 Z= 0.236 Angle : 0.588 5.587 23733 Z= 0.330 Chirality : 0.045 0.141 2556 Planarity : 0.005 0.044 3087 Dihedral : 5.257 20.710 2406 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.54 % Allowed : 7.57 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2112 helix: 1.32 (0.29), residues: 324 sheet: -0.01 (0.18), residues: 720 loop : 0.32 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 136 TYR 0.017 0.002 TYR C 441 PHE 0.023 0.002 PHE A 287 TRP 0.015 0.002 TRP C 539 HIS 0.007 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00506 (17463) covalent geometry : angle 0.58771 (23709) SS BOND : bond 0.00786 ( 12) SS BOND : angle 0.87201 ( 24) hydrogen bonds : bond 0.05613 ( 695) hydrogen bonds : angle 6.06189 ( 2181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.904 Fit side-chains REVERT: A 132 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7609 (tpm170) REVERT: A 199 ASP cc_start: 0.8940 (m-30) cc_final: 0.8703 (m-30) REVERT: A 308 HIS cc_start: 0.8528 (p-80) cc_final: 0.8307 (p90) REVERT: B 132 ARG cc_start: 0.8429 (tpp80) cc_final: 0.7601 (tpm170) REVERT: B 308 HIS cc_start: 0.8551 (p-80) cc_final: 0.8265 (p90) REVERT: B 434 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (pp) REVERT: B 496 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8594 (mmpt) REVERT: B 679 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: B 695 LYS cc_start: 0.8315 (tptt) cc_final: 0.7230 (ptpt) REVERT: C 132 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7621 (tpm170) REVERT: C 320 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8645 (tttm) REVERT: C 515 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8121 (mtp180) REVERT: D 83 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.4363 (mtp) REVERT: D 102 LYS cc_start: 0.7940 (pttp) cc_final: 0.7714 (pttm) REVERT: F 102 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7379 (pttp) outliers start: 28 outliers final: 16 residues processed: 213 average time/residue: 0.7600 time to fit residues: 182.7339 Evaluate side-chains 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 515 ARG Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 692 HIS B 112 GLN B 141 ASN B 657 HIS C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110671 restraints weight = 19173.821| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.36 r_work: 0.3137 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17475 Z= 0.264 Angle : 0.616 6.163 23733 Z= 0.346 Chirality : 0.046 0.141 2556 Planarity : 0.006 0.048 3087 Dihedral : 5.387 20.735 2406 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.54 % Allowed : 8.17 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2112 helix: 1.26 (0.29), residues: 324 sheet: -0.04 (0.18), residues: 720 loop : 0.26 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 136 TYR 0.018 0.002 TYR B 380 PHE 0.024 0.002 PHE A 287 TRP 0.015 0.003 TRP C 539 HIS 0.008 0.002 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00568 (17463) covalent geometry : angle 0.61607 (23709) SS BOND : bond 0.00879 ( 12) SS BOND : angle 0.93196 ( 24) hydrogen bonds : bond 0.05779 ( 695) hydrogen bonds : angle 6.17389 ( 2181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.880 Fit side-chains REVERT: A 132 ARG cc_start: 0.8404 (tpp80) cc_final: 0.7612 (tpm170) REVERT: A 199 ASP cc_start: 0.8939 (m-30) cc_final: 0.8703 (m-30) REVERT: A 308 HIS cc_start: 0.8528 (p-80) cc_final: 0.8307 (p90) REVERT: B 132 ARG cc_start: 0.8440 (tpp80) cc_final: 0.7620 (tpm170) REVERT: B 308 HIS cc_start: 0.8550 (p-80) cc_final: 0.8272 (p90) REVERT: B 434 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8379 (pp) REVERT: B 496 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8607 (mmpt) REVERT: B 502 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: B 679 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: B 695 LYS cc_start: 0.8309 (tptt) cc_final: 0.7236 (ptpt) REVERT: C 132 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7623 (tpm170) REVERT: C 320 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (tttm) REVERT: C 493 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7101 (pt0) REVERT: C 515 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8140 (mtp180) REVERT: D 83 MET cc_start: 0.4845 (mtp) cc_final: 0.4026 (mtp) REVERT: D 102 LYS cc_start: 0.7945 (pttp) cc_final: 0.7726 (pttm) REVERT: F 102 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7374 (pttp) outliers start: 28 outliers final: 15 residues processed: 213 average time/residue: 0.7163 time to fit residues: 172.2200 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 515 ARG Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 112 GLN B 141 ASN B 657 HIS C 112 GLN C 141 ASN C 308 HIS C 580 ASN C 657 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114242 restraints weight = 19188.704| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.67 r_work: 0.3162 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17475 Z= 0.143 Angle : 0.506 4.555 23733 Z= 0.285 Chirality : 0.042 0.144 2556 Planarity : 0.004 0.043 3087 Dihedral : 4.925 20.340 2406 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.59 % Allowed : 8.33 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2112 helix: 1.47 (0.29), residues: 324 sheet: -0.01 (0.18), residues: 720 loop : 0.36 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 715 TYR 0.014 0.001 TYR B 380 PHE 0.019 0.002 PHE A 287 TRP 0.014 0.002 TRP A 539 HIS 0.007 0.002 HIS C 657 Details of bonding type rmsd covalent geometry : bond 0.00290 (17463) covalent geometry : angle 0.50575 (23709) SS BOND : bond 0.00491 ( 12) SS BOND : angle 0.64947 ( 24) hydrogen bonds : bond 0.04768 ( 695) hydrogen bonds : angle 5.80846 ( 2181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.910 Fit side-chains REVERT: A 132 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7522 (tpm170) REVERT: A 199 ASP cc_start: 0.8965 (m-30) cc_final: 0.8721 (m-30) REVERT: A 308 HIS cc_start: 0.8518 (p-80) cc_final: 0.8291 (p90) REVERT: B 132 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7616 (tpm170) REVERT: B 308 HIS cc_start: 0.8557 (p-80) cc_final: 0.8253 (p90) REVERT: B 496 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8607 (mmpt) REVERT: B 695 LYS cc_start: 0.8283 (tptt) cc_final: 0.7195 (ptpt) REVERT: C 132 ARG cc_start: 0.8491 (tpp80) cc_final: 0.7581 (tpm170) REVERT: C 320 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8626 (tttm) REVERT: C 493 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: D 102 LYS cc_start: 0.7874 (pttp) cc_final: 0.7648 (pttm) REVERT: F 102 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7297 (pttp) outliers start: 29 outliers final: 16 residues processed: 218 average time/residue: 0.7385 time to fit residues: 181.9370 Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 112 GLN C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.177405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110680 restraints weight = 19247.049| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.38 r_work: 0.3151 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17475 Z= 0.245 Angle : 0.597 5.745 23733 Z= 0.334 Chirality : 0.046 0.140 2556 Planarity : 0.005 0.046 3087 Dihedral : 5.275 20.341 2406 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.26 % Allowed : 8.88 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2112 helix: 1.32 (0.29), residues: 324 sheet: -0.03 (0.18), residues: 720 loop : 0.31 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.018 0.002 TYR B 380 PHE 0.023 0.002 PHE A 287 TRP 0.016 0.003 TRP A 539 HIS 0.007 0.002 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00525 (17463) covalent geometry : angle 0.59612 (23709) SS BOND : bond 0.00819 ( 12) SS BOND : angle 0.90965 ( 24) hydrogen bonds : bond 0.05629 ( 695) hydrogen bonds : angle 6.07583 ( 2181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.889 Fit side-chains REVERT: A 132 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7622 (tpm170) REVERT: A 199 ASP cc_start: 0.8928 (m-30) cc_final: 0.8691 (m-30) REVERT: A 308 HIS cc_start: 0.8531 (p-80) cc_final: 0.8304 (p90) REVERT: B 132 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7609 (tpm170) REVERT: B 308 HIS cc_start: 0.8557 (p-80) cc_final: 0.8275 (p90) REVERT: B 496 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8606 (mmpt) REVERT: B 679 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: B 695 LYS cc_start: 0.8284 (tptt) cc_final: 0.7226 (ptpt) REVERT: C 132 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7613 (tpm170) REVERT: C 320 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8640 (tttm) REVERT: C 493 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: D 102 LYS cc_start: 0.7938 (pttp) cc_final: 0.7708 (pttm) REVERT: F 102 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7380 (pttp) outliers start: 23 outliers final: 14 residues processed: 209 average time/residue: 0.8017 time to fit residues: 188.5935 Evaluate side-chains 216 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 679 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain C residue 624 ARG Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 156 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 112 GLN C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112821 restraints weight = 19265.571| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.44 r_work: 0.3185 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17475 Z= 0.137 Angle : 0.502 4.760 23733 Z= 0.283 Chirality : 0.042 0.147 2556 Planarity : 0.004 0.043 3087 Dihedral : 4.883 20.173 2406 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.04 % Allowed : 9.27 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2112 helix: 1.46 (0.29), residues: 324 sheet: -0.01 (0.19), residues: 720 loop : 0.37 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 715 TYR 0.016 0.001 TYR B 380 PHE 0.018 0.002 PHE A 287 TRP 0.014 0.002 TRP A 539 HIS 0.007 0.002 HIS C 657 Details of bonding type rmsd covalent geometry : bond 0.00279 (17463) covalent geometry : angle 0.50183 (23709) SS BOND : bond 0.00447 ( 12) SS BOND : angle 0.63641 ( 24) hydrogen bonds : bond 0.04699 ( 695) hydrogen bonds : angle 5.77432 ( 2181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.870 Fit side-chains REVERT: A 132 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7484 (tpm170) REVERT: A 199 ASP cc_start: 0.8942 (m-30) cc_final: 0.8690 (m-30) REVERT: A 308 HIS cc_start: 0.8502 (p-80) cc_final: 0.8276 (p90) REVERT: B 132 ARG cc_start: 0.8431 (tpp80) cc_final: 0.7581 (tpm170) REVERT: B 308 HIS cc_start: 0.8529 (p-80) cc_final: 0.8235 (p90) REVERT: B 496 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8606 (mmpt) REVERT: B 695 LYS cc_start: 0.8262 (tptt) cc_final: 0.7191 (ptpt) REVERT: C 132 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7546 (tpm170) REVERT: C 320 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8606 (tttm) REVERT: C 493 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7097 (pt0) REVERT: F 102 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7274 (pttp) outliers start: 19 outliers final: 13 residues processed: 211 average time/residue: 0.7932 time to fit residues: 188.6716 Evaluate side-chains 215 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 493 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 16 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 141 ASN B 112 GLN B 141 ASN B 580 ASN B 657 HIS C 112 GLN C 141 ASN C 308 HIS C 657 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.181343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115077 restraints weight = 19331.231| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.42 r_work: 0.3216 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17475 Z= 0.110 Angle : 0.470 4.654 23733 Z= 0.263 Chirality : 0.041 0.143 2556 Planarity : 0.004 0.042 3087 Dihedral : 4.588 19.688 2406 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.88 % Allowed : 9.48 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2112 helix: 1.57 (0.29), residues: 324 sheet: 0.07 (0.19), residues: 681 loop : 0.40 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.014 0.001 TYR B 380 PHE 0.015 0.001 PHE A 287 TRP 0.013 0.001 TRP A 354 HIS 0.009 0.001 HIS C 657 Details of bonding type rmsd covalent geometry : bond 0.00220 (17463) covalent geometry : angle 0.46941 (23709) SS BOND : bond 0.00360 ( 12) SS BOND : angle 0.58015 ( 24) hydrogen bonds : bond 0.04242 ( 695) hydrogen bonds : angle 5.54093 ( 2181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14044.97 seconds wall clock time: 238 minutes 35.57 seconds (14315.57 seconds total)