Starting phenix.real_space_refine on Tue Nov 19 04:46:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_40583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_40583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_40583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_40583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sly_40583/11_2024/8sly_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-5513/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: 15.57, per 1000 atoms: 0.85 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: 5.03 Conformation dependent library (CDL) restraints added in 3.1 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: 1.84 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: 7.95 Time building geometry restraints manager: 5.79 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: 6.140 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: 0.000 Extract box with map and model: 3.160 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.840 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.960 ------------------------------------------------------------------------------- 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= 0.397 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 *********************** 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 : 2.212 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: 0.2751 time to fit residues: 101.7494 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 : 2.407 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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= 0.308 Angle : 0.563 7.456 25504 Z= 0.278 Chirality : 0.038 0.193 2976 Planarity : 0.004 0.037 3100 Dihedral : 8.996 81.065 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 *********************** 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 : 2.011 Fit side-chains REVERT: A 349 ASP cc_start: 0.8857 (t70) cc_final: 0.8620 (t0) REVERT: C 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8658 (t0) REVERT: D 349 ASP cc_start: 0.8870 (t70) cc_final: 0.8641 (t0) REVERT: D 384 GLU cc_start: 0.7848 (mp0) cc_final: 0.7631 (mp0) outliers start: 22 outliers final: 15 residues processed: 177 average time/residue: 0.2432 time to fit residues: 72.7139 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 : 2.116 ------------------------------------------------------------------------------- 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 119 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 0.4980 chunk 212 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18704 Z= 0.229 Angle : 0.508 7.468 25504 Z= 0.246 Chirality : 0.036 0.129 2976 Planarity : 0.003 0.038 3100 Dihedral : 7.580 71.212 2800 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.56 % Allowed : 9.61 % Favored : 88.83 % 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: 2.07 (0.18), residues: 2316 helix: 2.44 (0.14), residues: 1388 sheet: 0.43 (0.52), residues: 112 loop : -0.39 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 454 HIS 0.003 0.001 HIS D 313 PHE 0.014 0.001 PHE A 407 TYR 0.014 0.001 TYR A 471 ARG 0.003 0.000 ARG B 459 *********************** 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 188 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 2.089 Fit side-chains REVERT: A 349 ASP cc_start: 0.8864 (t70) cc_final: 0.8606 (t0) REVERT: A 638 LEU cc_start: 0.9394 (tt) cc_final: 0.9054 (tt) REVERT: B 638 LEU cc_start: 0.9390 (tt) cc_final: 0.9050 (tt) REVERT: B 645 MET cc_start: 0.8191 (mmm) cc_final: 0.7596 (mmt) REVERT: C 349 ASP cc_start: 0.8870 (t70) cc_final: 0.8623 (t0) REVERT: C 645 MET cc_start: 0.8232 (mmm) cc_final: 0.7938 (mmt) REVERT: D 349 ASP cc_start: 0.8875 (t70) cc_final: 0.8641 (t0) REVERT: D 638 LEU cc_start: 0.9383 (tt) cc_final: 0.9141 (tt) REVERT: D 645 MET cc_start: 0.8270 (mmm) cc_final: 0.7936 (mmt) outliers start: 27 outliers final: 19 residues processed: 177 average time/residue: 0.2423 time to fit residues: 72.9276 Evaluate side-chains 165 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 402 VAL 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 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 224 ASP Chi-restraints excluded: chain D residue 478 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 HIS B 487 GLN C 438 HIS C 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2300 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= 0.184 Angle : 0.485 7.682 25504 Z= 0.234 Chirality : 0.036 0.121 2976 Planarity : 0.003 0.039 3100 Dihedral : 7.194 69.141 2800 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 10.94 % Favored : 86.81 % 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: 2.19 (0.18), residues: 2316 helix: 2.59 (0.14), residues: 1388 sheet: 0.44 (0.52), residues: 112 loop : -0.43 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 454 HIS 0.003 0.001 HIS D 313 PHE 0.014 0.001 PHE D 407 TYR 0.011 0.001 TYR A 471 ARG 0.001 0.000 ARG B 459 *********************** 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 195 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 2.312 Fit side-chains REVERT: A 349 ASP cc_start: 0.8845 (t70) cc_final: 0.8597 (t0) REVERT: A 638 LEU cc_start: 0.9379 (tt) cc_final: 0.9099 (tt) REVERT: B 645 MET cc_start: 0.8225 (mmm) cc_final: 0.7648 (mmt) REVERT: C 349 ASP cc_start: 0.8859 (t70) cc_final: 0.8620 (t0) REVERT: C 645 MET cc_start: 0.8138 (mmm) cc_final: 0.7930 (mmt) REVERT: D 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8611 (t0) REVERT: D 638 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9107 (tt) REVERT: D 645 MET cc_start: 0.8118 (mmm) cc_final: 0.7806 (mmt) outliers start: 39 outliers final: 20 residues processed: 183 average time/residue: 0.2431 time to fit residues: 77.1348 Evaluate side-chains 165 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 624 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 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 Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 5.9990 chunk 129 optimal weight: 0.0370 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 HIS A 487 GLN D 438 HIS D 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 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 : 0.003 0.033 18704 Z= 0.171 Angle : 0.481 7.648 25504 Z= 0.230 Chirality : 0.035 0.121 2976 Planarity : 0.003 0.038 3100 Dihedral : 6.855 67.228 2800 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.31 % Allowed : 10.65 % Favored : 87.04 % 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: 2.34 (0.18), residues: 2316 helix: 2.72 (0.14), residues: 1384 sheet: 0.43 (0.51), residues: 112 loop : -0.39 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 454 HIS 0.002 0.000 HIS D 313 PHE 0.012 0.001 PHE A 407 TYR 0.010 0.001 TYR A 471 ARG 0.001 0.000 ARG A 459 *********************** 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 209 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 1.930 Fit side-chains REVERT: A 144 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8820 (pttp) REVERT: A 349 ASP cc_start: 0.8856 (t70) cc_final: 0.8610 (t0) REVERT: A 638 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9094 (tt) REVERT: B 638 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 645 MET cc_start: 0.8214 (mmm) cc_final: 0.7871 (mmt) REVERT: C 349 ASP cc_start: 0.8865 (t70) cc_final: 0.8613 (t0) REVERT: D 349 ASP cc_start: 0.8854 (t70) cc_final: 0.8618 (t0) REVERT: D 638 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9083 (tt) outliers start: 40 outliers final: 26 residues processed: 200 average time/residue: 0.2533 time to fit residues: 83.8233 Evaluate side-chains 185 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 2.068 ------------------------------------------------------------------------------- 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 521 HIS Chi-restraints excluded: chain A residue 542 LEU 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 521 HIS Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 638 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 521 HIS 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 521 HIS Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 632 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 76 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18704 Z= 0.126 Angle : 0.477 7.658 25504 Z= 0.225 Chirality : 0.035 0.112 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.516 65.540 2800 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.45 % Allowed : 12.04 % Favored : 86.52 % 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: 2.39 (0.18), residues: 2316 helix: 2.77 (0.14), residues: 1388 sheet: 0.56 (0.52), residues: 112 loop : -0.41 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 454 HIS 0.002 0.000 HIS B 165 PHE 0.012 0.001 PHE B 407 TYR 0.007 0.001 TYR A 471 ARG 0.001 0.000 ARG A 459 *********************** 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 210 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 2.501 Fit side-chains REVERT: A 349 ASP cc_start: 0.8832 (t70) cc_final: 0.8583 (t0) REVERT: A 638 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9096 (tp) REVERT: B 638 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9065 (tt) REVERT: C 349 ASP cc_start: 0.8846 (t70) cc_final: 0.8593 (t0) REVERT: D 349 ASP cc_start: 0.8849 (t70) cc_final: 0.8608 (t0) REVERT: D 638 LEU cc_start: 0.9336 (tt) cc_final: 0.9126 (tp) outliers start: 25 outliers final: 18 residues processed: 203 average time/residue: 0.2389 time to fit residues: 82.2971 Evaluate side-chains 189 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 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 638 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.0570 chunk 192 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18704 Z= 0.127 Angle : 0.462 8.723 25504 Z= 0.218 Chirality : 0.035 0.126 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.234 63.038 2800 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 12.67 % Favored : 85.94 % 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: 2.49 (0.18), residues: 2316 helix: 2.89 (0.14), residues: 1384 sheet: 0.60 (0.52), residues: 112 loop : -0.43 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 454 HIS 0.002 0.000 HIS D 165 PHE 0.011 0.001 PHE B 407 TYR 0.008 0.001 TYR A 471 ARG 0.003 0.000 ARG C 280 *********************** 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 206 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 144 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8869 (pttp) REVERT: A 349 ASP cc_start: 0.8835 (t70) cc_final: 0.8596 (t0) REVERT: A 638 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9136 (tp) REVERT: B 638 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 349 ASP cc_start: 0.8844 (t70) cc_final: 0.8607 (t0) REVERT: D 349 ASP cc_start: 0.8841 (t70) cc_final: 0.8600 (t0) REVERT: D 638 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9113 (tp) REVERT: D 645 MET cc_start: 0.8038 (mmt) cc_final: 0.7742 (tpt) outliers start: 24 outliers final: 17 residues processed: 201 average time/residue: 0.2483 time to fit residues: 84.7823 Evaluate side-chains 193 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 2.005 ------------------------------------------------------------------------------- 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 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 LEU 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 638 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 144 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 178 optimal weight: 0.0970 chunk 206 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18704 Z= 0.125 Angle : 0.467 9.004 25504 Z= 0.219 Chirality : 0.035 0.112 2976 Planarity : 0.003 0.036 3100 Dihedral : 6.066 61.037 2800 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.91 % Allowed : 12.44 % Favored : 85.65 % 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: 0.62 (0.53), residues: 112 loop : -0.44 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 454 HIS 0.002 0.000 HIS D 165 PHE 0.011 0.001 PHE D 407 TYR 0.007 0.001 TYR A 471 ARG 0.002 0.000 ARG B 280 *********************** 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 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 2.057 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8834 (t70) cc_final: 0.8590 (t0) REVERT: A 615 GLN cc_start: 0.8312 (pm20) cc_final: 0.8035 (pp30) REVERT: A 638 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9137 (tp) REVERT: B 638 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9120 (tp) REVERT: C 349 ASP cc_start: 0.8839 (t70) cc_final: 0.8597 (t0) REVERT: D 349 ASP cc_start: 0.8825 (t70) cc_final: 0.8591 (t0) REVERT: D 638 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9117 (tp) outliers start: 33 outliers final: 23 residues processed: 204 average time/residue: 0.2361 time to fit residues: 81.9723 Evaluate side-chains 201 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 2.175 ------------------------------------------------------------------------------- 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 624 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 638 LEU 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 546 VAL 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 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 452 GLN Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 536 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18704 Z= 0.374 Angle : 0.610 9.559 25504 Z= 0.290 Chirality : 0.039 0.174 2976 Planarity : 0.004 0.036 3100 Dihedral : 7.090 63.657 2800 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.91 % Allowed : 12.50 % Favored : 85.59 % 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: 2.12 (0.18), residues: 2316 helix: 2.54 (0.14), residues: 1388 sheet: 0.30 (0.51), residues: 112 loop : -0.47 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 454 HIS 0.005 0.001 HIS A 165 PHE 0.018 0.002 PHE D 407 TYR 0.016 0.002 TYR D 228 ARG 0.002 0.000 ARG B 684 *********************** 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 189 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 2.295 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8866 (t70) cc_final: 0.8629 (t0) REVERT: A 638 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9198 (tt) REVERT: B 638 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9170 (tp) REVERT: C 349 ASP cc_start: 0.8864 (t70) cc_final: 0.8620 (t0) REVERT: D 349 ASP cc_start: 0.8868 (t70) cc_final: 0.8635 (t0) REVERT: D 638 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9194 (tt) outliers start: 33 outliers final: 21 residues processed: 181 average time/residue: 0.2559 time to fit residues: 76.1892 Evaluate side-chains 169 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 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 546 VAL 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 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 Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18704 Z= 0.179 Angle : 0.527 9.960 25504 Z= 0.247 Chirality : 0.036 0.127 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.567 65.663 2800 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.45 % Allowed : 12.91 % Favored : 85.65 % 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: 2.33 (0.18), residues: 2316 helix: 2.74 (0.14), residues: 1384 sheet: 0.41 (0.51), residues: 112 loop : -0.42 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 454 HIS 0.003 0.000 HIS A 165 PHE 0.013 0.001 PHE D 407 TYR 0.009 0.001 TYR A 471 ARG 0.003 0.000 ARG A 280 ********************** 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 191 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 2.109 Fit side-chains revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8855 (t70) cc_final: 0.8612 (t0) REVERT: A 638 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9174 (tt) REVERT: B 638 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9147 (tp) REVERT: C 349 ASP cc_start: 0.8853 (t70) cc_final: 0.8613 (t0) REVERT: D 349 ASP cc_start: 0.8862 (t70) cc_final: 0.8621 (t0) REVERT: D 638 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9173 (tt) outliers start: 25 outliers final: 22 residues processed: 183 average time/residue: 0.2557 time to fit residues: 77.2210 Evaluate side-chains 185 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 TYR 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 624 LEU Chi-restraints excluded: chain A residue 638 LEU 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 546 VAL 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 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 Chi-restraints excluded: chain D residue 638 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 0.0270 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077380 restraints weight = 38782.750| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.24 r_work: 0.2904 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18704 Z= 0.215 Angle : 0.540 10.073 25504 Z= 0.253 Chirality : 0.037 0.269 2976 Planarity : 0.003 0.037 3100 Dihedral : 6.520 64.786 2800 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.45 % Allowed : 13.19 % 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: 2.28 (0.18), residues: 2316 helix: 2.71 (0.14), residues: 1380 sheet: 0.34 (0.51), residues: 112 loop : -0.45 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 454 HIS 0.003 0.001 HIS A 165 PHE 0.014 0.001 PHE D 407 TYR 0.011 0.001 TYR A 471 ARG 0.003 0.000 ARG D 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.23 seconds wall clock time: 63 minutes 45.62 seconds (3825.62 seconds total)