Starting phenix.real_space_refine on Mon Jun 16 09:03:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.map" model { file = "/net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sly_40583/06_2025/8sly_40583.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 1 4.78 5 C 12092 2.51 5 N 3028 2.21 5 O 3044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18257 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4486 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 18, 'TRANS': 572} Chain breaks: 5 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 227 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Unusual residues: {' NA': 1, 'P0T': 2, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 11.46, per 1000 atoms: 0.63 Number of scatterers: 18257 At special positions: 0 Unit cell: (156.04, 156.04, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Na 1 11.00 O 3044 8.00 N 3028 7.00 C 12092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.30 Conformation dependent library (CDL) restraints added in 2.3 seconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 65.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.677A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 374' Processing helix chain 'A' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 433 through 459 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 527 through 560 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 672 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.676A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 375 through 389 removed outlier: 3.505A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 433 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 Processing helix chain 'B' and resid 527 through 560 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.676A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 433 through 459 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.904A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 519 Processing helix chain 'C' and resid 527 through 560 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 672 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.666A pdb=" N LYS D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.657A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.677A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 369 through 374 removed outlier: 4.025A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 374' Processing helix chain 'D' and resid 375 through 389 removed outlier: 3.506A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 433 through 459 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.698A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.903A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.129A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 Processing helix chain 'D' and resid 527 through 560 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.671A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.690A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.298A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.299A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3072 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: 6.59 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2949 1.32 - 1.45: 5167 1.45 - 1.57: 10428 1.57 - 1.69: 32 1.69 - 1.82: 128 Bond restraints: 18704 Sorted by residual: bond pdb=" C05 P0T C 801 " pdb=" C06 P0T C 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C05 P0T D 801 " pdb=" C06 P0T D 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C05 P0T A 801 " pdb=" C06 P0T A 801 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C05 P0T B 801 " pdb=" C06 P0T B 801 " ideal model delta sigma weight residual 1.521 1.656 -0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C03 P0T C 801 " pdb=" C04 P0T C 801 " ideal model delta sigma weight residual 1.548 1.679 -0.131 2.00e-02 2.50e+03 4.30e+01 ... (remaining 18699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 24966 1.99 - 3.98: 382 3.98 - 5.98: 112 5.98 - 7.97: 28 7.97 - 9.96: 16 Bond angle restraints: 25504 Sorted by residual: angle pdb=" N ILE A 605 " pdb=" CA ILE A 605 " pdb=" C ILE A 605 " ideal model delta sigma weight residual 112.98 108.73 4.25 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE D 605 " pdb=" CA ILE D 605 " pdb=" C ILE D 605 " ideal model delta sigma weight residual 112.98 108.74 4.24 1.25e+00 6.40e-01 1.15e+01 angle pdb=" N ILE B 605 " pdb=" CA ILE B 605 " pdb=" C ILE B 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" N ILE C 605 " pdb=" CA ILE C 605 " pdb=" C ILE C 605 " ideal model delta sigma weight residual 112.98 108.76 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" C22 POV D 803 " pdb=" C21 POV D 803 " pdb=" O21 POV D 803 " ideal model delta sigma weight residual 111.03 120.99 -9.96 3.00e+00 1.11e-01 1.10e+01 ... (remaining 25499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 10448 27.39 - 54.78: 396 54.78 - 82.17: 40 82.17 - 109.55: 4 109.55 - 136.94: 8 Dihedral angle restraints: 10896 sinusoidal: 3980 harmonic: 6916 Sorted by residual: dihedral pdb=" C18 P0T B 801 " pdb=" C20 P0T B 801 " pdb=" C21 P0T B 801 " pdb=" C22 P0T B 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.35 136.94 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T C 801 " pdb=" C20 P0T C 801 " pdb=" C21 P0T C 801 " pdb=" C22 P0T C 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C18 P0T A 801 " pdb=" C20 P0T A 801 " pdb=" C21 P0T A 801 " pdb=" C22 P0T A 801 " ideal model delta sinusoidal sigma weight residual 179.29 42.36 136.93 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 10893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2949 0.112 - 0.223: 19 0.223 - 0.335: 0 0.335 - 0.447: 0 0.447 - 0.559: 8 Chirality restraints: 2976 Sorted by residual: chirality pdb=" C03 P0T C 802 " pdb=" C04 P0T C 802 " pdb=" C05 P0T C 802 " pdb=" C10 P0T C 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T A 802 " pdb=" C04 P0T A 802 " pdb=" C05 P0T A 802 " pdb=" C10 P0T A 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 chirality pdb=" C03 P0T B 802 " pdb=" C04 P0T B 802 " pdb=" C05 P0T B 802 " pdb=" C10 P0T B 802 " both_signs ideal model delta sigma weight residual False -2.55 -3.11 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 2973 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 604 " -0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR C 604 " 0.029 2.00e-02 2.50e+03 pdb=" O THR C 604 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE C 605 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 604 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C THR A 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR A 604 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 605 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 604 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 604 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 604 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 605 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1759 2.74 - 3.28: 18065 3.28 - 3.82: 30255 3.82 - 4.36: 35197 4.36 - 4.90: 60802 Nonbonded interactions: 146078 Sorted by model distance: nonbonded pdb=" OH TYR C 544 " pdb=" OG1 THR C 604 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR D 544 " pdb=" OG1 THR D 604 " model vdw 2.206 3.040 nonbonded pdb=" OH TYR B 544 " pdb=" OG1 THR B 604 " model vdw 2.206 3.040 nonbonded pdb=" O ALA D 361 " pdb=" NH1 ARG D 369 " model vdw 2.302 3.120 ... (remaining 146073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 728 or resid 801 through 802)) selection = (chain 'B' and (resid 75 through 728 or resid 801 through 802)) selection = (chain 'C' and (resid 75 through 728 or resid 801 through 802)) selection = (chain 'D' and (resid 75 through 728 or resid 801 through 802)) } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.980 Check model and map are aligned: 0.470 Set scattering table: 0.620 Process input model: 41.890 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.006 0.136 18704 Z= 0.320 Angle : 0.665 9.959 25504 Z= 0.297 Chirality : 0.046 0.559 2976 Planarity : 0.003 0.047 3100 Dihedral : 15.008 136.942 6416 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2316 helix: 1.76 (0.14), residues: 1376 sheet: 0.44 (0.50), residues: 112 loop : -0.50 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 454 HIS 0.001 0.000 HIS D 413 PHE 0.023 0.001 PHE C 362 TYR 0.016 0.001 TYR B 162 ARG 0.006 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.24036 ( 1080) hydrogen bonds : angle 6.01926 ( 3072) covalent geometry : bond 0.00627 (18704) covalent geometry : angle 0.66479 (25504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.988 Fit side-chains REVERT: A 349 ASP cc_start: 0.8840 (t70) cc_final: 0.8586 (t0) REVERT: B 349 ASP cc_start: 0.8910 (t70) cc_final: 0.8687 (t0) REVERT: C 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8649 (t0) REVERT: D 349 ASP cc_start: 0.8880 (t70) cc_final: 0.8628 (t0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2353 time to fit residues: 87.8940 Evaluate side-chains 166 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 5.9990 chunk 178 optimal weight: 0.0980 chunk 99 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 413 HIS B 127 ASN B 413 HIS C 127 ASN D 127 ASN D 413 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076626 restraints weight = 38838.343| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.26 r_work: 0.2896 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18704 Z= 0.202 Angle : 0.563 7.456 25504 Z= 0.278 Chirality : 0.038 0.193 2976 Planarity : 0.004 0.037 3100 Dihedral : 8.996 81.068 2800 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.27 % Allowed : 7.35 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.18), residues: 2316 helix: 2.33 (0.14), residues: 1384 sheet: 0.62 (0.52), residues: 112 loop : -0.42 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 454 HIS 0.004 0.001 HIS B 313 PHE 0.017 0.001 PHE C 407 TYR 0.017 0.002 TYR A 471 ARG 0.003 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 1080) hydrogen bonds : angle 3.69310 ( 3072) covalent geometry : bond 0.00475 (18704) covalent geometry : angle 0.56285 (25504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.914 Fit side-chains REVERT: A 349 ASP cc_start: 0.9343 (t70) cc_final: 0.9061 (t0) REVERT: B 349 ASP cc_start: 0.9348 (t70) cc_final: 0.9101 (t0) REVERT: C 349 ASP cc_start: 0.9327 (t70) cc_final: 0.9078 (t0) REVERT: D 349 ASP cc_start: 0.9335 (t70) cc_final: 0.9058 (t0) REVERT: D 384 GLU cc_start: 0.8616 (mp0) cc_final: 0.8263 (mp0) outliers start: 22 outliers final: 15 residues processed: 177 average time/residue: 0.2255 time to fit residues: 68.3578 Evaluate side-chains 162 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 55 optimal weight: 0.0970 chunk 33 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079600 restraints weight = 38542.955| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.27 r_work: 0.2953 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18704 Z= 0.098 Angle : 0.471 7.572 25504 Z= 0.226 Chirality : 0.035 0.112 2976 Planarity : 0.003 0.037 3100 Dihedral : 7.433 70.440 2800 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.56 % Allowed : 9.03 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2316 helix: 2.52 (0.14), residues: 1388 sheet: 0.59 (0.53), residues: 112 loop : -0.43 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 454 HIS 0.002 0.000 HIS C 313 PHE 0.013 0.001 PHE A 407 TYR 0.011 0.001 TYR A 471 ARG 0.002 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1080) hydrogen bonds : angle 3.30863 ( 3072) covalent geometry : bond 0.00225 (18704) covalent geometry : angle 0.47062 (25504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 2.117 Fit side-chains REVERT: A 349 ASP cc_start: 0.9312 (t70) cc_final: 0.9011 (t0) REVERT: A 638 LEU cc_start: 0.9386 (tt) cc_final: 0.9067 (tt) REVERT: B 349 ASP cc_start: 0.9314 (t70) cc_final: 0.9031 (t0) REVERT: B 638 LEU cc_start: 0.9397 (tt) cc_final: 0.9114 (tt) REVERT: B 645 MET cc_start: 0.9333 (mmm) cc_final: 0.8925 (mmt) REVERT: C 349 ASP cc_start: 0.9309 (t70) cc_final: 0.9007 (t0) REVERT: C 645 MET cc_start: 0.9372 (mmm) cc_final: 0.9078 (mmt) REVERT: D 349 ASP cc_start: 0.9310 (t70) cc_final: 0.9031 (t0) REVERT: D 638 LEU cc_start: 0.9384 (tt) cc_final: 0.9177 (tt) REVERT: D 645 MET cc_start: 0.9373 (mmm) cc_final: 0.9095 (mmt) outliers start: 27 outliers final: 13 residues processed: 195 average time/residue: 0.2298 time to fit residues: 78.9695 Evaluate side-chains 165 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 150 optimal weight: 5.9990 chunk 176 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 228 optimal weight: 0.8980 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 HIS C 438 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078951 restraints weight = 38510.739| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.27 r_work: 0.2940 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18704 Z= 0.105 Angle : 0.472 7.726 25504 Z= 0.227 Chirality : 0.035 0.124 2976 Planarity : 0.003 0.038 3100 Dihedral : 6.970 69.164 2800 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.39 % Allowed : 11.05 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.18), residues: 2316 helix: 2.70 (0.14), residues: 1388 sheet: 0.66 (0.53), residues: 112 loop : -0.45 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 454 HIS 0.002 0.000 HIS D 313 PHE 0.013 0.001 PHE B 407 TYR 0.011 0.001 TYR A 471 ARG 0.002 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 1080) hydrogen bonds : angle 3.16797 ( 3072) covalent geometry : bond 0.00245 (18704) covalent geometry : angle 0.47248 (25504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 3.081 Fit side-chains REVERT: A 349 ASP cc_start: 0.9305 (t70) cc_final: 0.9012 (t0) REVERT: B 349 ASP cc_start: 0.9298 (t70) cc_final: 0.9024 (t0) REVERT: B 645 MET cc_start: 0.9354 (mmm) cc_final: 0.9061 (mmt) REVERT: C 349 ASP cc_start: 0.9303 (t70) cc_final: 0.9029 (t0) REVERT: D 349 ASP cc_start: 0.9291 (t70) cc_final: 0.9001 (t0) REVERT: D 526 SER cc_start: 0.8817 (t) cc_final: 0.8605 (p) outliers start: 24 outliers final: 17 residues processed: 187 average time/residue: 0.2495 time to fit residues: 79.3367 Evaluate side-chains 179 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 191 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076413 restraints weight = 39011.312| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.26 r_work: 0.2890 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18704 Z= 0.157 Angle : 0.515 7.227 25504 Z= 0.248 Chirality : 0.036 0.140 2976 Planarity : 0.003 0.038 3100 Dihedral : 7.109 71.202 2800 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.43 % Allowed : 11.34 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.18), residues: 2316 helix: 2.68 (0.14), residues: 1388 sheet: 0.35 (0.51), residues: 112 loop : -0.43 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 454 HIS 0.003 0.001 HIS C 313 PHE 0.014 0.001 PHE A 407 TYR 0.013 0.001 TYR A 471 ARG 0.002 0.000 ARG D 684 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 1080) hydrogen bonds : angle 3.23200 ( 3072) covalent geometry : bond 0.00374 (18704) covalent geometry : angle 0.51518 (25504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 2.246 Fit side-chains REVERT: A 349 ASP cc_start: 0.9322 (t70) cc_final: 0.9036 (t0) REVERT: A 638 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9215 (tp) REVERT: B 349 ASP cc_start: 0.9319 (t70) cc_final: 0.9034 (t0) REVERT: B 384 GLU cc_start: 0.8789 (mp0) cc_final: 0.8586 (mp0) REVERT: B 485 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9376 (tt) REVERT: B 638 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9190 (tt) REVERT: C 349 ASP cc_start: 0.9315 (t70) cc_final: 0.9032 (t0) REVERT: C 485 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9358 (tt) REVERT: D 349 ASP cc_start: 0.9323 (t70) cc_final: 0.9031 (t0) REVERT: D 638 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9211 (tp) outliers start: 42 outliers final: 23 residues processed: 194 average time/residue: 0.3218 time to fit residues: 105.4888 Evaluate side-chains 180 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 71 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 60 optimal weight: 40.0000 chunk 217 optimal weight: 4.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 HIS D 487 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077338 restraints weight = 38898.926| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.26 r_work: 0.2910 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18704 Z= 0.126 Angle : 0.502 7.997 25504 Z= 0.239 Chirality : 0.036 0.127 2976 Planarity : 0.003 0.038 3100 Dihedral : 6.863 67.071 2800 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.97 % Allowed : 12.50 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.18), residues: 2316 helix: 2.69 (0.14), residues: 1388 sheet: 0.36 (0.51), residues: 112 loop : -0.43 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 454 HIS 0.003 0.001 HIS C 313 PHE 0.013 0.001 PHE A 407 TYR 0.010 0.001 TYR A 471 ARG 0.002 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 1080) hydrogen bonds : angle 3.18271 ( 3072) covalent geometry : bond 0.00298 (18704) covalent geometry : angle 0.50191 (25504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 2.647 Fit side-chains REVERT: A 144 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8902 (pttp) REVERT: A 349 ASP cc_start: 0.9315 (t70) cc_final: 0.9023 (t0) REVERT: A 638 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9220 (tp) REVERT: B 349 ASP cc_start: 0.9315 (t70) cc_final: 0.9024 (t0) REVERT: B 384 GLU cc_start: 0.8818 (mp0) cc_final: 0.8597 (mp0) REVERT: C 349 ASP cc_start: 0.9313 (t70) cc_final: 0.9023 (t0) REVERT: D 349 ASP cc_start: 0.9310 (t70) cc_final: 0.9019 (t0) REVERT: D 638 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9217 (tp) outliers start: 34 outliers final: 23 residues processed: 187 average time/residue: 0.4016 time to fit residues: 128.5962 Evaluate side-chains 181 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 185 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 chunk 160 optimal weight: 0.0870 chunk 165 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 183 optimal weight: 0.0980 chunk 154 optimal weight: 0.1980 overall best weight: 0.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS A 452 GLN B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081198 restraints weight = 38380.882| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.25 r_work: 0.2983 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18704 Z= 0.080 Angle : 0.460 7.782 25504 Z= 0.217 Chirality : 0.034 0.112 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.277 63.172 2800 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.50 % Allowed : 13.25 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.18), residues: 2316 helix: 2.84 (0.14), residues: 1388 sheet: 0.58 (0.53), residues: 112 loop : -0.41 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 454 HIS 0.002 0.000 HIS B 165 PHE 0.010 0.001 PHE D 407 TYR 0.006 0.001 TYR C 514 ARG 0.003 0.000 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.02725 ( 1080) hydrogen bonds : angle 3.05503 ( 3072) covalent geometry : bond 0.00173 (18704) covalent geometry : angle 0.45969 (25504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.888 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9260 (t70) cc_final: 0.8973 (t0) REVERT: A 638 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9172 (tp) REVERT: B 349 ASP cc_start: 0.9257 (t70) cc_final: 0.8980 (t0) REVERT: C 349 ASP cc_start: 0.9267 (t70) cc_final: 0.8984 (t0) REVERT: D 349 ASP cc_start: 0.9259 (t70) cc_final: 0.8981 (t0) outliers start: 26 outliers final: 19 residues processed: 214 average time/residue: 0.2328 time to fit residues: 84.3754 Evaluate side-chains 199 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 227 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 172 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.079922 restraints weight = 38485.754| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.21 r_work: 0.2965 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18704 Z= 0.099 Angle : 0.497 9.733 25504 Z= 0.232 Chirality : 0.035 0.163 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.196 61.766 2800 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.68 % Allowed : 12.96 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2316 helix: 2.90 (0.14), residues: 1388 sheet: 0.57 (0.52), residues: 112 loop : -0.41 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 454 HIS 0.002 0.000 HIS B 165 PHE 0.012 0.001 PHE A 407 TYR 0.008 0.001 TYR A 471 ARG 0.002 0.000 ARG D 280 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 1080) hydrogen bonds : angle 3.03755 ( 3072) covalent geometry : bond 0.00234 (18704) covalent geometry : angle 0.49735 (25504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9256 (t70) cc_final: 0.8986 (t0) REVERT: A 638 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9199 (tt) REVERT: B 349 ASP cc_start: 0.9254 (t70) cc_final: 0.8993 (t0) REVERT: C 349 ASP cc_start: 0.9255 (t70) cc_final: 0.9005 (t0) REVERT: C 638 LEU cc_start: 0.9393 (tt) cc_final: 0.9156 (tt) REVERT: D 144 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8898 (pttp) REVERT: D 349 ASP cc_start: 0.9246 (t70) cc_final: 0.8979 (t0) outliers start: 29 outliers final: 20 residues processed: 203 average time/residue: 0.2235 time to fit residues: 77.9359 Evaluate side-chains 196 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 180 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 234 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078737 restraints weight = 38747.890| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.27 r_work: 0.2934 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18704 Z= 0.114 Angle : 0.493 8.588 25504 Z= 0.231 Chirality : 0.035 0.119 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.241 60.677 2800 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.50 % Allowed : 13.08 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2316 helix: 2.89 (0.14), residues: 1388 sheet: 0.61 (0.52), residues: 112 loop : -0.41 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 454 HIS 0.003 0.001 HIS B 165 PHE 0.013 0.001 PHE A 407 TYR 0.010 0.001 TYR A 471 ARG 0.002 0.000 ARG D 280 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 1080) hydrogen bonds : angle 3.05200 ( 3072) covalent geometry : bond 0.00270 (18704) covalent geometry : angle 0.49342 (25504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 1.954 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.9294 (t70) cc_final: 0.9005 (t0) REVERT: A 638 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9205 (tt) REVERT: B 349 ASP cc_start: 0.9272 (t70) cc_final: 0.8995 (t0) REVERT: C 349 ASP cc_start: 0.9276 (t70) cc_final: 0.8999 (t0) REVERT: C 638 LEU cc_start: 0.9383 (tt) cc_final: 0.9140 (tt) REVERT: D 144 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8886 (pttp) REVERT: D 349 ASP cc_start: 0.9294 (t70) cc_final: 0.8999 (t0) outliers start: 26 outliers final: 21 residues processed: 191 average time/residue: 0.2339 time to fit residues: 75.2402 Evaluate side-chains 186 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 452 GLN Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 232 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 228 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080525 restraints weight = 38425.687| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.21 r_work: 0.2973 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18704 Z= 0.088 Angle : 0.486 10.223 25504 Z= 0.226 Chirality : 0.035 0.116 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.041 59.859 2800 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.27 % Allowed : 13.31 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.18), residues: 2316 helix: 2.91 (0.14), residues: 1388 sheet: 0.61 (0.52), residues: 112 loop : -0.42 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 454 HIS 0.002 0.000 HIS B 165 PHE 0.011 0.001 PHE D 407 TYR 0.008 0.001 TYR D 447 ARG 0.003 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.02795 ( 1080) hydrogen bonds : angle 3.01824 ( 3072) covalent geometry : bond 0.00201 (18704) covalent geometry : angle 0.48596 (25504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8863 (pttp) REVERT: A 349 ASP cc_start: 0.9241 (t70) cc_final: 0.8966 (t0) REVERT: A 638 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9209 (tp) REVERT: B 349 ASP cc_start: 0.9236 (t70) cc_final: 0.8967 (t0) REVERT: C 349 ASP cc_start: 0.9242 (t70) cc_final: 0.8981 (t0) REVERT: D 144 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8848 (pttp) REVERT: D 349 ASP cc_start: 0.9249 (t70) cc_final: 0.8988 (t0) outliers start: 22 outliers final: 20 residues processed: 195 average time/residue: 0.2303 time to fit residues: 76.0081 Evaluate side-chains 200 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 0.0040 chunk 213 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.079111 restraints weight = 38601.530| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.24 r_work: 0.2938 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18704 Z= 0.113 Angle : 0.517 12.635 25504 Z= 0.239 Chirality : 0.035 0.118 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.085 58.799 2800 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.22 % Allowed : 13.37 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.18), residues: 2316 helix: 2.90 (0.14), residues: 1388 sheet: 0.59 (0.52), residues: 112 loop : -0.42 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 454 HIS 0.003 0.001 HIS B 165 PHE 0.012 0.001 PHE D 407 TYR 0.010 0.001 TYR A 471 ARG 0.003 0.000 ARG B 280 Details of bonding type rmsd hydrogen bonds : bond 0.02957 ( 1080) hydrogen bonds : angle 3.06748 ( 3072) covalent geometry : bond 0.00269 (18704) covalent geometry : angle 0.51677 (25504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9927.08 seconds wall clock time: 175 minutes 23.04 seconds (10523.04 seconds total)