Starting phenix.real_space_refine on Fri Sep 27 12:17:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u6p_8512/09_2024/5u6p_8512.cif" } resolution = 3.51 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 10156 2.51 5 N 2688 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15640 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3793 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 16, 'TRANS': 487} Chain breaks: 2 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 174 Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Restraints were copied for chains: G, F, H, C, B, D Time building chain proxies: 8.47, per 1000 atoms: 0.54 Number of scatterers: 15640 At special positions: 0 Unit cell: (123.5, 123.5, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 2676 8.00 N 2688 7.00 C 10156 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 79.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 removed outlier: 3.640A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 139 through 167 Proline residue: A 161 - end of helix removed outlier: 3.534A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.934A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.646A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.509A pdb=" N ASP A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.810A pdb=" N ILE A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 Processing helix chain 'A' and resid 292 through 323 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.518A pdb=" N ASN A 334 " --> pdb=" O TRP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'A' and resid 368 through 401 Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.674A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.570A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 removed outlier: 3.661A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 491 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.678A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.934A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'E' and resid 2 through 19 Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 139 through 167 Proline residue: B 161 - end of helix removed outlier: 3.534A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.508A pdb=" N ASP B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.811A pdb=" N ILE B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 290 Processing helix chain 'B' and resid 292 through 323 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.519A pdb=" N ASN B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 368 through 401 Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.675A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.572A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 491 removed outlier: 3.663A pdb=" N LYS B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 491 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 546 Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.678A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.932A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'F' and resid 2 through 19 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 139 through 167 Proline residue: C 161 - end of helix removed outlier: 3.533A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.509A pdb=" N ASP C 225 " --> pdb=" O TRP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.810A pdb=" N ILE C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 290 Processing helix chain 'C' and resid 292 through 323 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.519A pdb=" N ASN C 334 " --> pdb=" O TRP C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'C' and resid 368 through 401 Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.676A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.571A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 466 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.939A pdb=" N ALA C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.662A pdb=" N LYS C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 491 " --> pdb=" O MET C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 546 Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.679A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.933A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'G' and resid 2 through 19 Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 139 through 167 Proline residue: D 161 - end of helix removed outlier: 3.534A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.935A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 219 removed outlier: 3.648A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.507A pdb=" N ASP D 225 " --> pdb=" O TRP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.811A pdb=" N ILE D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 290 Processing helix chain 'D' and resid 292 through 323 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 335 removed outlier: 3.518A pdb=" N ASN D 334 " --> pdb=" O TRP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 368 through 401 Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.679A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.571A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 466 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.940A pdb=" N ALA D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 491 removed outlier: 3.662A pdb=" N LYS D 490 " --> pdb=" O ALA D 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 491 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 546 Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.677A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.932A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 608 Processing helix chain 'H' and resid 2 through 19 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR A 562 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 515 " --> pdb=" O TYR A 562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.751A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 492 through 496 Processing sheet with id=AA5, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.690A pdb=" N TYR B 562 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE B 515 " --> pdb=" O TYR B 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.752A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 496 Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.689A pdb=" N TYR C 562 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE C 515 " --> pdb=" O TYR C 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.750A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 492 through 496 Processing sheet with id=AB2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.688A pdb=" N TYR D 562 " --> pdb=" O ILE D 515 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE D 515 " --> pdb=" O TYR D 562 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.751A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3468 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: 5.09 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4708 1.34 - 1.46: 2376 1.46 - 1.57: 8720 1.57 - 1.69: 8 1.69 - 1.81: 204 Bond restraints: 16016 Sorted by residual: bond pdb=" CA ILE C 160 " pdb=" CB ILE C 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" CA ILE B 160 " pdb=" CB ILE B 160 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.34e+01 bond pdb=" CA ILE D 160 " pdb=" CB ILE D 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.27e+01 bond pdb=" CA ILE A 160 " pdb=" CB ILE A 160 " ideal model delta sigma weight residual 1.539 1.558 -0.019 5.40e-03 3.43e+04 1.19e+01 bond pdb=" C SER C 346 " pdb=" O SER C 346 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.15e-02 7.56e+03 1.15e+01 ... (remaining 16011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17624 1.97 - 3.94: 4006 3.94 - 5.91: 154 5.91 - 7.88: 12 7.88 - 9.85: 4 Bond angle restraints: 21800 Sorted by residual: angle pdb=" O ILE D 160 " pdb=" C ILE D 160 " pdb=" N PRO D 161 " ideal model delta sigma weight residual 120.42 124.84 -4.42 6.40e-01 2.44e+00 4.77e+01 angle pdb=" O ILE A 160 " pdb=" C ILE A 160 " pdb=" N PRO A 161 " ideal model delta sigma weight residual 120.42 124.81 -4.39 6.40e-01 2.44e+00 4.70e+01 angle pdb=" O ILE C 160 " pdb=" C ILE C 160 " pdb=" N PRO C 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O ILE B 160 " pdb=" C ILE B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 120.42 124.79 -4.37 6.40e-01 2.44e+00 4.66e+01 angle pdb=" O THR D 173 " pdb=" C THR D 173 " pdb=" N PRO D 174 " ideal model delta sigma weight residual 120.38 125.11 -4.73 7.90e-01 1.60e+00 3.59e+01 ... (remaining 21795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 9304 31.61 - 63.21: 64 63.21 - 94.82: 0 94.82 - 126.43: 0 126.43 - 158.03: 12 Dihedral angle restraints: 9380 sinusoidal: 3224 harmonic: 6156 Sorted by residual: dihedral pdb=" C5' CMP D 901 " pdb=" O5' CMP D 901 " pdb=" P CMP D 901 " pdb=" O1P CMP D 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.97 -158.03 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP C 901 " pdb=" O5' CMP C 901 " pdb=" P CMP C 901 " pdb=" O1P CMP C 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.98 -158.02 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' CMP B 901 " pdb=" O5' CMP B 901 " pdb=" P CMP B 901 " pdb=" O1P CMP B 901 " ideal model delta sinusoidal sigma weight residual 60.00 -141.99 -158.01 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1587 0.057 - 0.114: 591 0.114 - 0.171: 229 0.171 - 0.228: 51 0.228 - 0.285: 26 Chirality restraints: 2484 Sorted by residual: chirality pdb=" CA HIS D 279 " pdb=" N HIS D 279 " pdb=" C HIS D 279 " pdb=" CB HIS D 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA HIS B 279 " pdb=" N HIS B 279 " pdb=" C HIS B 279 " pdb=" CB HIS B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE C 186 " pdb=" N PHE C 186 " pdb=" C PHE C 186 " pdb=" CB PHE C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2481 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO D 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 319 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 320 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 319 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 320 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 320 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 320 " 0.059 5.00e-02 4.00e+02 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5775 2.90 - 3.40: 16994 3.40 - 3.90: 25277 3.90 - 4.40: 28759 4.40 - 4.90: 45760 Nonbonded interactions: 122565 Sorted by model distance: nonbonded pdb=" O LYS C 261 " pdb=" OG SER C 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS D 261 " pdb=" OG SER D 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS A 261 " pdb=" OG SER A 264 " model vdw 2.399 3.040 nonbonded pdb=" O LYS B 261 " pdb=" OG SER B 264 " model vdw 2.400 3.040 nonbonded pdb=" O ASP C 225 " pdb=" OG SER C 228 " model vdw 2.447 3.040 ... (remaining 122560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 36.850 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 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 : 0.007 0.044 16016 Z= 0.485 Angle : 1.410 9.850 21800 Z= 1.084 Chirality : 0.073 0.285 2484 Planarity : 0.006 0.112 2748 Dihedral : 12.411 158.034 5388 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.31 (0.17), residues: 1992 helix: 1.89 (0.12), residues: 1380 sheet: 0.47 (0.47), residues: 100 loop : -1.97 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 281 HIS 0.008 0.002 HIS D 437 PHE 0.027 0.002 PHE A 569 TYR 0.027 0.002 TYR C 411 ARG 0.005 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ILE cc_start: 0.8142 (mt) cc_final: 0.7785 (tt) REVERT: A 234 TYR cc_start: 0.6663 (m-80) cc_final: 0.5665 (t80) REVERT: A 236 PHE cc_start: 0.8369 (t80) cc_final: 0.8137 (t80) REVERT: A 439 TYR cc_start: 0.6267 (m-80) cc_final: 0.6007 (m-80) REVERT: B 135 ILE cc_start: 0.8309 (mt) cc_final: 0.8069 (tt) REVERT: B 152 MET cc_start: 0.6683 (mmm) cc_final: 0.6314 (tpt) REVERT: B 234 TYR cc_start: 0.6469 (m-80) cc_final: 0.5524 (t80) REVERT: B 445 ASP cc_start: 0.6626 (t0) cc_final: 0.6413 (p0) REVERT: B 482 ASN cc_start: 0.8055 (m110) cc_final: 0.7673 (t0) REVERT: B 485 THR cc_start: 0.8331 (m) cc_final: 0.8108 (p) REVERT: C 135 ILE cc_start: 0.8233 (mt) cc_final: 0.7939 (tt) REVERT: C 152 MET cc_start: 0.6730 (mmm) cc_final: 0.6341 (tpt) REVERT: C 217 TYR cc_start: 0.6281 (t80) cc_final: 0.6046 (t80) REVERT: C 234 TYR cc_start: 0.6468 (m-80) cc_final: 0.5654 (t80) REVERT: C 287 MET cc_start: 0.6196 (mmm) cc_final: 0.5872 (mmt) REVERT: C 336 MET cc_start: 0.7088 (ptm) cc_final: 0.6883 (ptp) REVERT: C 445 ASP cc_start: 0.6820 (t0) cc_final: 0.6513 (p0) REVERT: D 135 ILE cc_start: 0.8345 (mt) cc_final: 0.8092 (tt) REVERT: D 152 MET cc_start: 0.6796 (mmm) cc_final: 0.6433 (tpt) REVERT: D 217 TYR cc_start: 0.5843 (t80) cc_final: 0.5615 (t80) REVERT: D 233 ASP cc_start: 0.6993 (p0) cc_final: 0.6099 (p0) REVERT: D 234 TYR cc_start: 0.6374 (m-80) cc_final: 0.5615 (t80) REVERT: D 336 MET cc_start: 0.7020 (ptm) cc_final: 0.6819 (ptp) REVERT: D 445 ASP cc_start: 0.6655 (t0) cc_final: 0.6452 (p0) REVERT: D 482 ASN cc_start: 0.7800 (m110) cc_final: 0.7434 (m-40) REVERT: D 485 THR cc_start: 0.8419 (m) cc_final: 0.8207 (p) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.2691 time to fit residues: 205.6527 Evaluate side-chains 338 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.0170 chunk 61 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 421 HIS B 398 GLN C 398 GLN D 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16016 Z= 0.197 Angle : 0.582 7.889 21800 Z= 0.310 Chirality : 0.041 0.147 2484 Planarity : 0.005 0.066 2748 Dihedral : 11.902 167.722 2304 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.27 % Allowed : 10.65 % Favored : 87.07 % 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: 2.88 (0.19), residues: 1992 helix: 3.14 (0.13), residues: 1420 sheet: -0.03 (0.44), residues: 96 loop : -1.77 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 281 HIS 0.006 0.001 HIS B 432 PHE 0.032 0.002 PHE D 186 TYR 0.020 0.001 TYR B 411 ARG 0.011 0.001 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 395 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.6709 (p0) cc_final: 0.5934 (p0) REVERT: A 234 TYR cc_start: 0.6694 (m-80) cc_final: 0.5686 (t80) REVERT: A 236 PHE cc_start: 0.8382 (t80) cc_final: 0.8147 (t80) REVERT: A 289 TYR cc_start: 0.5736 (m-80) cc_final: 0.5309 (m-10) REVERT: A 439 TYR cc_start: 0.6318 (m-80) cc_final: 0.5845 (m-80) REVERT: A 530 MET cc_start: 0.5040 (mpp) cc_final: 0.4826 (mpp) REVERT: B 140 ASP cc_start: 0.7448 (m-30) cc_final: 0.7119 (t0) REVERT: B 217 TYR cc_start: 0.5669 (t80) cc_final: 0.5448 (t80) REVERT: B 234 TYR cc_start: 0.6455 (m-80) cc_final: 0.5487 (t80) REVERT: B 482 ASN cc_start: 0.8058 (m110) cc_final: 0.7622 (t0) REVERT: C 234 TYR cc_start: 0.6542 (m-80) cc_final: 0.5720 (t80) REVERT: C 482 ASN cc_start: 0.7723 (m110) cc_final: 0.7484 (m-40) REVERT: D 234 TYR cc_start: 0.6390 (m-80) cc_final: 0.5581 (t80) REVERT: D 445 ASP cc_start: 0.6479 (t0) cc_final: 0.6175 (t0) REVERT: D 482 ASN cc_start: 0.7948 (m110) cc_final: 0.7518 (m-40) outliers start: 32 outliers final: 16 residues processed: 405 average time/residue: 0.2181 time to fit residues: 139.5743 Evaluate side-chains 358 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 342 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 30.0000 chunk 57 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 51 optimal weight: 30.0000 chunk 185 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 517 HIS B 421 HIS B 517 HIS C 179 ASN C 421 HIS D 300 ASN D 421 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16016 Z= 0.193 Angle : 0.561 14.848 21800 Z= 0.283 Chirality : 0.039 0.149 2484 Planarity : 0.004 0.052 2748 Dihedral : 11.716 170.986 2304 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.06 % Allowed : 12.50 % Favored : 85.44 % 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: 2.80 (0.19), residues: 1992 helix: 2.97 (0.13), residues: 1432 sheet: 0.36 (0.50), residues: 96 loop : -1.65 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 281 HIS 0.014 0.001 HIS D 432 PHE 0.019 0.001 PHE B 569 TYR 0.026 0.001 TYR A 217 ARG 0.007 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 362 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 234 TYR cc_start: 0.6795 (m-80) cc_final: 0.5772 (t80) REVERT: A 236 PHE cc_start: 0.8255 (t80) cc_final: 0.8023 (t80) REVERT: A 289 TYR cc_start: 0.5790 (m-80) cc_final: 0.5407 (m-10) REVERT: B 225 ASP cc_start: 0.7261 (m-30) cc_final: 0.6950 (m-30) REVERT: B 234 TYR cc_start: 0.6396 (m-80) cc_final: 0.5447 (t80) REVERT: B 482 ASN cc_start: 0.7966 (m110) cc_final: 0.7739 (m-40) REVERT: C 234 TYR cc_start: 0.6526 (m-80) cc_final: 0.5673 (t80) REVERT: C 482 ASN cc_start: 0.7835 (m110) cc_final: 0.7593 (m-40) REVERT: C 517 HIS cc_start: 0.6662 (m-70) cc_final: 0.6410 (m90) REVERT: D 225 ASP cc_start: 0.7283 (m-30) cc_final: 0.6953 (m-30) REVERT: D 234 TYR cc_start: 0.6372 (m-80) cc_final: 0.5594 (t80) REVERT: D 482 ASN cc_start: 0.7794 (m110) cc_final: 0.7567 (m-40) outliers start: 29 outliers final: 21 residues processed: 371 average time/residue: 0.2118 time to fit residues: 125.1123 Evaluate side-chains 344 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 323 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 0.0270 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN C 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16016 Z= 0.186 Angle : 0.533 9.829 21800 Z= 0.270 Chirality : 0.038 0.146 2484 Planarity : 0.004 0.059 2748 Dihedral : 11.608 170.947 2304 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 14.70 % Favored : 83.24 % 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: 2.77 (0.19), residues: 1992 helix: 2.90 (0.13), residues: 1420 sheet: 0.59 (0.53), residues: 96 loop : -1.40 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 281 HIS 0.009 0.001 HIS D 432 PHE 0.016 0.001 PHE B 226 TYR 0.020 0.001 TYR A 217 ARG 0.007 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 346 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 TYR cc_start: 0.6775 (m-80) cc_final: 0.5753 (t80) REVERT: A 236 PHE cc_start: 0.8278 (t80) cc_final: 0.8053 (t80) REVERT: A 289 TYR cc_start: 0.5866 (m-80) cc_final: 0.5457 (m-10) REVERT: B 225 ASP cc_start: 0.7593 (m-30) cc_final: 0.7333 (m-30) REVERT: B 234 TYR cc_start: 0.6413 (m-80) cc_final: 0.5637 (t80) REVERT: B 287 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5890 (tpt) REVERT: B 482 ASN cc_start: 0.7950 (m110) cc_final: 0.7710 (m-40) REVERT: C 140 ASP cc_start: 0.7508 (m-30) cc_final: 0.7265 (t0) REVERT: C 217 TYR cc_start: 0.5708 (t80) cc_final: 0.5449 (t80) REVERT: C 234 TYR cc_start: 0.6646 (m-80) cc_final: 0.5698 (t80) REVERT: C 482 ASN cc_start: 0.7851 (m110) cc_final: 0.7617 (m-40) REVERT: C 517 HIS cc_start: 0.6623 (m-70) cc_final: 0.6389 (m90) REVERT: D 225 ASP cc_start: 0.7611 (m-30) cc_final: 0.7317 (m-30) REVERT: D 234 TYR cc_start: 0.6527 (m-80) cc_final: 0.5719 (t80) REVERT: D 482 ASN cc_start: 0.7847 (m110) cc_final: 0.7628 (m-40) outliers start: 29 outliers final: 21 residues processed: 358 average time/residue: 0.2307 time to fit residues: 131.1292 Evaluate side-chains 353 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 331 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16016 Z= 0.220 Angle : 0.535 11.252 21800 Z= 0.273 Chirality : 0.038 0.156 2484 Planarity : 0.004 0.047 2748 Dihedral : 11.549 168.916 2304 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.77 % Allowed : 14.77 % Favored : 82.46 % 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: 2.82 (0.19), residues: 1992 helix: 2.88 (0.13), residues: 1424 sheet: 0.65 (0.54), residues: 96 loop : -1.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 281 HIS 0.005 0.001 HIS D 432 PHE 0.030 0.001 PHE B 569 TYR 0.019 0.001 TYR D 411 ARG 0.005 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 353 time to evaluate : 1.839 Fit side-chains REVERT: A 234 TYR cc_start: 0.6852 (m-80) cc_final: 0.5858 (t80) REVERT: A 236 PHE cc_start: 0.8253 (t80) cc_final: 0.8018 (t80) REVERT: B 234 TYR cc_start: 0.6665 (m-80) cc_final: 0.5717 (t80) REVERT: B 482 ASN cc_start: 0.7940 (m110) cc_final: 0.7708 (m-40) REVERT: C 234 TYR cc_start: 0.6664 (m-80) cc_final: 0.5721 (t80) REVERT: C 482 ASN cc_start: 0.7803 (m110) cc_final: 0.7570 (m-40) REVERT: C 517 HIS cc_start: 0.6617 (m-70) cc_final: 0.6369 (m90) REVERT: D 234 TYR cc_start: 0.6635 (m-80) cc_final: 0.5695 (t80) REVERT: D 482 ASN cc_start: 0.7811 (m110) cc_final: 0.7585 (m-40) outliers start: 39 outliers final: 32 residues processed: 368 average time/residue: 0.2171 time to fit residues: 126.3832 Evaluate side-chains 351 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 197 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16016 Z= 0.235 Angle : 0.535 7.926 21800 Z= 0.276 Chirality : 0.038 0.146 2484 Planarity : 0.004 0.043 2748 Dihedral : 11.571 170.107 2304 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.77 % Allowed : 15.70 % Favored : 81.53 % 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: 2.77 (0.19), residues: 1992 helix: 2.79 (0.13), residues: 1428 sheet: 0.65 (0.54), residues: 96 loop : -1.11 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 281 HIS 0.003 0.001 HIS D 355 PHE 0.034 0.001 PHE B 569 TYR 0.018 0.001 TYR D 411 ARG 0.006 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 343 time to evaluate : 1.906 Fit side-chains REVERT: A 234 TYR cc_start: 0.6855 (m-80) cc_final: 0.5865 (t80) REVERT: A 236 PHE cc_start: 0.8236 (t80) cc_final: 0.7988 (t80) REVERT: B 234 TYR cc_start: 0.6670 (m-80) cc_final: 0.5737 (t80) REVERT: B 287 MET cc_start: 0.5911 (tpt) cc_final: 0.5691 (tpt) REVERT: B 482 ASN cc_start: 0.7938 (m110) cc_final: 0.7696 (m-40) REVERT: C 234 TYR cc_start: 0.6660 (m-80) cc_final: 0.5729 (t80) REVERT: C 287 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5629 (tpt) REVERT: C 482 ASN cc_start: 0.7797 (m110) cc_final: 0.7565 (m-40) REVERT: C 517 HIS cc_start: 0.6608 (m-70) cc_final: 0.6364 (m90) REVERT: D 234 TYR cc_start: 0.6635 (m-80) cc_final: 0.5701 (t80) REVERT: D 482 ASN cc_start: 0.7788 (m110) cc_final: 0.7561 (m-40) outliers start: 39 outliers final: 31 residues processed: 357 average time/residue: 0.2134 time to fit residues: 122.6677 Evaluate side-chains 356 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 324 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 196 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 GLN C 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16016 Z= 0.171 Angle : 0.522 8.632 21800 Z= 0.266 Chirality : 0.037 0.159 2484 Planarity : 0.004 0.056 2748 Dihedral : 11.620 170.556 2304 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.27 % Allowed : 16.76 % Favored : 80.97 % 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: 2.79 (0.19), residues: 1992 helix: 2.79 (0.13), residues: 1428 sheet: 0.63 (0.54), residues: 96 loop : -1.01 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 281 HIS 0.003 0.000 HIS D 286 PHE 0.028 0.001 PHE B 569 TYR 0.020 0.001 TYR A 411 ARG 0.006 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 348 time to evaluate : 1.858 Fit side-chains REVERT: A 234 TYR cc_start: 0.6851 (m-80) cc_final: 0.5864 (t80) REVERT: A 236 PHE cc_start: 0.8221 (t80) cc_final: 0.7990 (t80) REVERT: B 234 TYR cc_start: 0.6653 (m-80) cc_final: 0.5736 (t80) REVERT: B 482 ASN cc_start: 0.7913 (m110) cc_final: 0.7692 (m-40) REVERT: C 217 TYR cc_start: 0.5923 (t80) cc_final: 0.5538 (t80) REVERT: C 234 TYR cc_start: 0.6654 (m-80) cc_final: 0.5721 (t80) REVERT: C 482 ASN cc_start: 0.7806 (m110) cc_final: 0.7561 (m-40) REVERT: C 517 HIS cc_start: 0.6614 (m-70) cc_final: 0.6355 (m90) REVERT: D 234 TYR cc_start: 0.6631 (m-80) cc_final: 0.5692 (t80) REVERT: D 459 GLU cc_start: 0.8209 (pt0) cc_final: 0.7985 (mm-30) REVERT: D 482 ASN cc_start: 0.7784 (m110) cc_final: 0.7549 (m-40) outliers start: 32 outliers final: 22 residues processed: 362 average time/residue: 0.2199 time to fit residues: 126.0223 Evaluate side-chains 360 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 338 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 154 optimal weight: 0.3980 chunk 178 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN D 516 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16016 Z= 0.212 Angle : 0.543 10.479 21800 Z= 0.275 Chirality : 0.038 0.160 2484 Planarity : 0.004 0.075 2748 Dihedral : 11.589 170.003 2304 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.13 % Allowed : 17.40 % Favored : 80.47 % 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: 2.68 (0.19), residues: 1992 helix: 2.69 (0.13), residues: 1440 sheet: 0.61 (0.53), residues: 96 loop : -1.08 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 281 HIS 0.004 0.001 HIS C 432 PHE 0.033 0.001 PHE D 569 TYR 0.020 0.001 TYR A 411 ARG 0.010 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 341 time to evaluate : 1.797 Fit side-chains REVERT: A 234 TYR cc_start: 0.6861 (m-80) cc_final: 0.5842 (t80) REVERT: A 236 PHE cc_start: 0.8248 (t80) cc_final: 0.8008 (t80) REVERT: B 234 TYR cc_start: 0.6668 (m-80) cc_final: 0.5774 (t80) REVERT: B 482 ASN cc_start: 0.7906 (m110) cc_final: 0.7672 (m-40) REVERT: C 234 TYR cc_start: 0.6711 (m-80) cc_final: 0.5746 (t80) REVERT: C 287 MET cc_start: 0.5926 (tpt) cc_final: 0.5663 (tpp) REVERT: C 482 ASN cc_start: 0.7775 (m110) cc_final: 0.7544 (m-40) REVERT: C 517 HIS cc_start: 0.6581 (m-70) cc_final: 0.6340 (m90) REVERT: D 234 TYR cc_start: 0.6679 (m-80) cc_final: 0.5694 (t80) REVERT: D 482 ASN cc_start: 0.7776 (m110) cc_final: 0.7543 (m-40) outliers start: 30 outliers final: 28 residues processed: 354 average time/residue: 0.2100 time to fit residues: 119.5761 Evaluate side-chains 346 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 318 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain D residue 385 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16016 Z= 0.208 Angle : 0.551 12.490 21800 Z= 0.277 Chirality : 0.038 0.186 2484 Planarity : 0.004 0.067 2748 Dihedral : 11.647 172.730 2304 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.99 % Allowed : 18.25 % Favored : 79.76 % 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: 2.65 (0.19), residues: 1992 helix: 2.64 (0.13), residues: 1436 sheet: 0.59 (0.53), residues: 96 loop : -1.00 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 281 HIS 0.003 0.001 HIS A 432 PHE 0.034 0.001 PHE D 569 TYR 0.020 0.001 TYR A 411 ARG 0.009 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 336 time to evaluate : 1.925 Fit side-chains REVERT: A 234 TYR cc_start: 0.6884 (m-80) cc_final: 0.5852 (t80) REVERT: A 236 PHE cc_start: 0.8243 (t80) cc_final: 0.8002 (t80) REVERT: A 482 ASN cc_start: 0.7447 (m110) cc_final: 0.7218 (m-40) REVERT: B 234 TYR cc_start: 0.6670 (m-80) cc_final: 0.5767 (t80) REVERT: B 482 ASN cc_start: 0.7887 (m110) cc_final: 0.7659 (m-40) REVERT: C 234 TYR cc_start: 0.6713 (m-80) cc_final: 0.5751 (t80) REVERT: C 236 PHE cc_start: 0.8537 (t80) cc_final: 0.8310 (t80) REVERT: C 287 MET cc_start: 0.6031 (tpt) cc_final: 0.5726 (tpp) REVERT: C 482 ASN cc_start: 0.7779 (m110) cc_final: 0.7538 (m-40) REVERT: C 517 HIS cc_start: 0.6582 (m-70) cc_final: 0.6341 (m90) REVERT: D 234 TYR cc_start: 0.6691 (m-80) cc_final: 0.5730 (t80) REVERT: D 482 ASN cc_start: 0.7769 (m110) cc_final: 0.7539 (m-40) outliers start: 28 outliers final: 25 residues processed: 350 average time/residue: 0.2117 time to fit residues: 118.9802 Evaluate side-chains 330 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 305 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.5387 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16016 Z= 0.186 Angle : 0.549 9.600 21800 Z= 0.276 Chirality : 0.038 0.184 2484 Planarity : 0.004 0.054 2748 Dihedral : 11.702 175.922 2304 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.63 % Allowed : 18.47 % Favored : 79.90 % 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: 2.61 (0.19), residues: 1992 helix: 2.61 (0.13), residues: 1436 sheet: 0.56 (0.54), residues: 96 loop : -0.99 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 281 HIS 0.004 0.001 HIS A 432 PHE 0.032 0.001 PHE D 569 TYR 0.017 0.001 TYR A 411 ARG 0.014 0.001 ARG A 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 342 time to evaluate : 1.875 Fit side-chains REVERT: A 234 TYR cc_start: 0.6885 (m-80) cc_final: 0.5845 (t80) REVERT: A 236 PHE cc_start: 0.8235 (t80) cc_final: 0.7997 (t80) REVERT: A 482 ASN cc_start: 0.7446 (m110) cc_final: 0.7217 (m-40) REVERT: B 234 TYR cc_start: 0.6717 (m-80) cc_final: 0.5761 (t80) REVERT: B 482 ASN cc_start: 0.7879 (m110) cc_final: 0.7630 (m-40) REVERT: C 234 TYR cc_start: 0.6791 (m-80) cc_final: 0.5822 (t80) REVERT: C 236 PHE cc_start: 0.8549 (t80) cc_final: 0.8316 (t80) REVERT: C 287 MET cc_start: 0.5920 (tpt) cc_final: 0.5623 (tpp) REVERT: C 482 ASN cc_start: 0.7775 (m110) cc_final: 0.7537 (m-40) REVERT: C 517 HIS cc_start: 0.6591 (m-70) cc_final: 0.6353 (m90) REVERT: D 234 TYR cc_start: 0.6675 (m-80) cc_final: 0.5722 (t80) REVERT: D 482 ASN cc_start: 0.7764 (m110) cc_final: 0.7532 (m-40) outliers start: 23 outliers final: 21 residues processed: 353 average time/residue: 0.2145 time to fit residues: 121.1833 Evaluate side-chains 353 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 332 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 0.0170 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.120189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095103 restraints weight = 30815.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097917 restraints weight = 15032.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099677 restraints weight = 9676.746| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16016 Z= 0.188 Angle : 0.560 10.294 21800 Z= 0.278 Chirality : 0.038 0.175 2484 Planarity : 0.004 0.052 2748 Dihedral : 11.711 177.299 2304 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.56 % Allowed : 19.03 % Favored : 79.40 % 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: 2.60 (0.19), residues: 1992 helix: 2.60 (0.13), residues: 1436 sheet: 0.55 (0.54), residues: 96 loop : -0.98 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 281 HIS 0.004 0.001 HIS D 286 PHE 0.032 0.001 PHE D 569 TYR 0.020 0.001 TYR A 411 ARG 0.007 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.31 seconds wall clock time: 57 minutes 22.86 seconds (3442.86 seconds total)