Starting phenix.real_space_refine on Mon Jul 22 04:49:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4m_41036/07_2024/8t4m_41036.cif" } resolution = 3.16 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= 0.001 sd= 0.027 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 140 5.16 5 C 10984 2.51 5 N 2864 2.21 5 O 3008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 436": "OE1" <-> "OE2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17000 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4228 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 9.56, per 1000 atoms: 0.56 Number of scatterers: 17000 At special positions: 0 Unit cell: (112.288, 112.288, 128.064, 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 140 16.00 P 4 15.00 O 3008 8.00 N 2864 7.00 C 10984 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 - 3.50 Amino acid : False - 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: 6.71 Conformation dependent library (CDL) restraints added in 3.4 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 73.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 107 through 114 Processing helix chain 'D' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 193 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 264 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 270 through 289 Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR D 407 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (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 480 through 489 Processing helix chain 'D' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP D 589 " --> pdb=" O THR D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS D 604 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 620 " --> pdb=" O ASN D 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'C' and resid 253 through 264 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 289 Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR C 407 " --> pdb=" O SER C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (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 480 through 489 Processing helix chain 'C' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 107 through 114 Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 212 through 218 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 270 through 289 Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (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 480 through 489 Processing helix chain 'B' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 107 through 114 Processing helix chain 'A' and resid 116 through 130 removed outlier: 3.506A pdb=" N ALA A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.704A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 289 Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.792A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.710A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.550A pdb=" N TYR A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.941A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (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 480 through 489 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.881A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.925A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.707A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 removed outlier: 3.930A pdb=" N LYS A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 620 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER D 204 " --> pdb=" O ASN D 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 503 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR D 524 " --> pdb=" O LYS D 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS D 528 " --> pdb=" O THR D 524 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 503 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR C 524 " --> pdb=" O LYS C 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS C 528 " --> pdb=" O THR C 524 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER B 204 " --> pdb=" O ASN B 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 503 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 524 " --> pdb=" O LYS B 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.771A pdb=" N SER A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.663A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.724A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 503 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR A 524 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LYS A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) 1149 hydrogen bonds defined for protein. 3363 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: 5.67 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5404 1.35 - 1.47: 4290 1.47 - 1.58: 7450 1.58 - 1.70: 8 1.70 - 1.82: 244 Bond restraints: 17396 Sorted by residual: bond pdb=" C3' CMP A 901 " pdb=" C4' CMP A 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP B 901 " pdb=" C4' CMP B 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP D 901 " pdb=" C4' CMP D 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" C3' CMP C 901 " pdb=" C4' CMP C 901 " ideal model delta sigma weight residual 1.521 1.500 0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" CA PRO D 577 " pdb=" C PRO D 577 " ideal model delta sigma weight residual 1.520 1.537 -0.018 1.42e-02 4.96e+03 1.52e+00 ... (remaining 17391 not shown) Histogram of bond angle deviations from ideal: 100.17 - 107.36: 540 107.36 - 114.55: 10164 114.55 - 121.74: 9420 121.74 - 128.94: 3292 128.94 - 136.13: 144 Bond angle restraints: 23560 Sorted by residual: angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CB MET A 215 " pdb=" CG MET A 215 " pdb=" SD MET A 215 " ideal model delta sigma weight residual 112.70 124.15 -11.45 3.00e+00 1.11e-01 1.46e+01 ... (remaining 23555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 9800 26.04 - 52.07: 500 52.07 - 78.11: 52 78.11 - 104.14: 4 104.14 - 130.18: 4 Dihedral angle restraints: 10360 sinusoidal: 4084 harmonic: 6276 Sorted by residual: dihedral pdb=" CA ASP C 209 " pdb=" C ASP C 209 " pdb=" N PRO C 210 " pdb=" CA PRO C 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP B 209 " pdb=" C ASP B 209 " pdb=" N PRO B 210 " pdb=" CA PRO B 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASP A 209 " pdb=" C ASP A 209 " pdb=" N PRO A 210 " pdb=" CA PRO A 210 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 10357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1551 0.024 - 0.049: 581 0.049 - 0.073: 348 0.073 - 0.097: 84 0.097 - 0.122: 64 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 2625 not shown) Planarity restraints: 2956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO C 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 480 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO D 481 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 481 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 481 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.03e+00 pdb=" N PRO B 481 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " 0.024 5.00e-02 4.00e+02 ... (remaining 2953 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2200 2.75 - 3.29: 16867 3.29 - 3.83: 28535 3.83 - 4.36: 31712 4.36 - 4.90: 57736 Nonbonded interactions: 137050 Sorted by model distance: nonbonded pdb=" NZ LYS D 108 " pdb=" OE2 GLU C 436 " model vdw 2.217 2.520 nonbonded pdb=" OE2 GLU D 436 " pdb=" NZ LYS A 108 " model vdw 2.217 2.520 nonbonded pdb=" NZ LYS B 108 " pdb=" OE2 GLU A 436 " model vdw 2.217 2.520 nonbonded pdb=" NZ LYS C 108 " pdb=" OE2 GLU B 436 " model vdw 2.217 2.520 nonbonded pdb=" OH TYR D 435 " pdb=" OE1 GLU A 452 " model vdw 2.240 2.440 ... (remaining 137045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.310 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 46.750 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.080 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.002 0.031 17396 Z= 0.140 Angle : 0.565 11.451 23560 Z= 0.283 Chirality : 0.037 0.122 2628 Planarity : 0.003 0.044 2956 Dihedral : 14.873 130.178 6296 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 14.06 % 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: 0.92 (0.18), residues: 2116 helix: 1.42 (0.13), residues: 1488 sheet: -0.12 (0.55), residues: 88 loop : -1.55 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 133 HIS 0.002 0.001 HIS C 421 PHE 0.005 0.001 PHE A 483 TYR 0.014 0.001 TYR D 576 ARG 0.002 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: D 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7723 (m-80) REVERT: D 454 ASN cc_start: 0.8443 (p0) cc_final: 0.8179 (p0) REVERT: C 118 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7531 (ptmm) REVERT: C 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7724 (m-80) REVERT: C 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: B 118 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7530 (ptmm) REVERT: B 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: B 454 ASN cc_start: 0.8442 (p0) cc_final: 0.8180 (p0) REVERT: A 118 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7532 (ptmm) REVERT: A 259 PHE cc_start: 0.8058 (m-80) cc_final: 0.7725 (m-80) REVERT: A 454 ASN cc_start: 0.8445 (p0) cc_final: 0.8179 (p0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2708 time to fit residues: 114.4599 Evaluate side-chains 256 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 101 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 HIS ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17396 Z= 0.237 Angle : 0.518 7.676 23560 Z= 0.262 Chirality : 0.040 0.156 2628 Planarity : 0.003 0.032 2956 Dihedral : 6.786 131.910 2372 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.76 % Allowed : 13.44 % Favored : 84.81 % 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: 1.41 (0.19), residues: 2116 helix: 1.81 (0.14), residues: 1496 sheet: -0.15 (0.54), residues: 88 loop : -1.44 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 281 HIS 0.003 0.001 HIS C 421 PHE 0.008 0.001 PHE B 514 TYR 0.011 0.001 TYR B 411 ARG 0.001 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 1.980 Fit side-chains REVERT: D 259 PHE cc_start: 0.8077 (m-80) cc_final: 0.7748 (m-80) REVERT: D 286 HIS cc_start: 0.7850 (OUTLIER) cc_final: 0.7559 (t-90) REVERT: D 524 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8018 (p) REVERT: D 581 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7848 (tpp80) REVERT: C 259 PHE cc_start: 0.8077 (m-80) cc_final: 0.7748 (m-80) REVERT: C 286 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: C 524 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8018 (p) REVERT: C 581 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7848 (tpp80) REVERT: B 259 PHE cc_start: 0.8078 (m-80) cc_final: 0.7748 (m-80) REVERT: B 286 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7561 (t-90) REVERT: B 524 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8018 (p) REVERT: B 581 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7849 (tpp80) REVERT: A 259 PHE cc_start: 0.8079 (m-80) cc_final: 0.7751 (m-80) REVERT: A 286 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: A 524 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8019 (p) REVERT: A 581 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7849 (tpp80) outliers start: 31 outliers final: 8 residues processed: 276 average time/residue: 0.2782 time to fit residues: 116.0328 Evaluate side-chains 248 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 232 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 0.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17396 Z= 0.147 Angle : 0.476 7.637 23560 Z= 0.239 Chirality : 0.038 0.154 2628 Planarity : 0.003 0.029 2956 Dihedral : 6.770 132.507 2372 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.81 % Allowed : 13.38 % Favored : 84.81 % 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: 1.73 (0.19), residues: 2116 helix: 2.05 (0.14), residues: 1504 sheet: 0.05 (0.55), residues: 88 loop : -1.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 281 HIS 0.003 0.001 HIS C 421 PHE 0.009 0.001 PHE B 514 TYR 0.011 0.001 TYR B 411 ARG 0.002 0.000 ARG D 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 264 time to evaluate : 1.929 Fit side-chains REVERT: D 108 LYS cc_start: 0.7957 (tptt) cc_final: 0.7625 (tptt) REVERT: D 259 PHE cc_start: 0.8063 (m-80) cc_final: 0.7725 (m-80) REVERT: D 286 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7567 (t-90) REVERT: D 524 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8015 (p) REVERT: D 581 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7780 (tpp80) REVERT: C 108 LYS cc_start: 0.7958 (tptt) cc_final: 0.7626 (tptt) REVERT: C 259 PHE cc_start: 0.8063 (m-80) cc_final: 0.7725 (m-80) REVERT: C 286 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7569 (t-90) REVERT: C 524 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8013 (p) REVERT: C 581 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7781 (tpp80) REVERT: B 108 LYS cc_start: 0.7957 (tptt) cc_final: 0.7626 (tptt) REVERT: B 259 PHE cc_start: 0.8063 (m-80) cc_final: 0.7728 (m-80) REVERT: B 286 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.7568 (t-90) REVERT: B 524 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8011 (p) REVERT: B 581 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7780 (tpp80) REVERT: A 108 LYS cc_start: 0.7957 (tptt) cc_final: 0.7613 (tptt) REVERT: A 259 PHE cc_start: 0.8064 (m-80) cc_final: 0.7730 (m-80) REVERT: A 286 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7569 (t-90) REVERT: A 524 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 581 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7778 (tpp80) outliers start: 32 outliers final: 16 residues processed: 284 average time/residue: 0.2508 time to fit residues: 111.3679 Evaluate side-chains 284 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17396 Z= 0.255 Angle : 0.508 7.916 23560 Z= 0.260 Chirality : 0.040 0.161 2628 Planarity : 0.003 0.039 2956 Dihedral : 6.749 131.585 2372 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.66 % Allowed : 13.38 % Favored : 83.96 % 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: 1.69 (0.19), residues: 2116 helix: 2.07 (0.14), residues: 1496 sheet: 0.06 (0.54), residues: 88 loop : -1.52 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 281 HIS 0.003 0.001 HIS D 392 PHE 0.010 0.001 PHE B 514 TYR 0.012 0.001 TYR B 411 ARG 0.002 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 1.857 Fit side-chains REVERT: D 259 PHE cc_start: 0.8084 (m-80) cc_final: 0.7759 (m-80) REVERT: D 286 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: D 523 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7776 (pt) REVERT: D 524 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.7902 (p) REVERT: D 581 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7835 (tpp80) REVERT: C 259 PHE cc_start: 0.8084 (m-80) cc_final: 0.7759 (m-80) REVERT: C 286 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7636 (t-90) REVERT: C 523 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7779 (pt) REVERT: C 524 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.7901 (p) REVERT: C 581 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7835 (tpp80) REVERT: B 259 PHE cc_start: 0.8086 (m-80) cc_final: 0.7762 (m-80) REVERT: B 286 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7637 (t-90) REVERT: B 523 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7778 (pt) REVERT: B 524 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 581 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7834 (tpp80) REVERT: A 259 PHE cc_start: 0.8086 (m-80) cc_final: 0.7764 (m-80) REVERT: A 286 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7639 (t-90) REVERT: A 523 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7779 (pt) REVERT: A 524 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 581 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7835 (tpp80) outliers start: 47 outliers final: 23 residues processed: 272 average time/residue: 0.2575 time to fit residues: 110.2753 Evaluate side-chains 271 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.201 Angle : 0.493 7.831 23560 Z= 0.249 Chirality : 0.039 0.163 2628 Planarity : 0.003 0.038 2956 Dihedral : 6.752 131.880 2372 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 14.00 % Favored : 83.96 % 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: 1.82 (0.19), residues: 2116 helix: 2.16 (0.14), residues: 1496 sheet: 0.09 (0.54), residues: 88 loop : -1.45 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 133 HIS 0.002 0.001 HIS C 421 PHE 0.018 0.001 PHE A 236 TYR 0.013 0.001 TYR D 411 ARG 0.001 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 1.977 Fit side-chains REVERT: D 113 MET cc_start: 0.8667 (mmm) cc_final: 0.8445 (mmm) REVERT: D 259 PHE cc_start: 0.8084 (m-80) cc_final: 0.7751 (m-80) REVERT: D 286 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: D 523 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7853 (pt) REVERT: D 524 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8183 (t) REVERT: D 581 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7890 (tpp80) REVERT: C 113 MET cc_start: 0.8669 (mmm) cc_final: 0.8446 (mmm) REVERT: C 259 PHE cc_start: 0.8083 (m-80) cc_final: 0.7751 (m-80) REVERT: C 286 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7656 (t-90) REVERT: C 523 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7853 (pt) REVERT: C 524 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8180 (t) REVERT: C 581 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7891 (tpp80) REVERT: B 113 MET cc_start: 0.8666 (mmm) cc_final: 0.8445 (mmm) REVERT: B 259 PHE cc_start: 0.8082 (m-80) cc_final: 0.7752 (m-80) REVERT: B 286 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7656 (t-90) REVERT: B 523 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7853 (pt) REVERT: B 524 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8179 (t) REVERT: B 581 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7889 (tpp80) REVERT: A 113 MET cc_start: 0.8662 (mmm) cc_final: 0.8442 (mmm) REVERT: A 259 PHE cc_start: 0.8083 (m-80) cc_final: 0.7753 (m-80) REVERT: A 286 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7658 (t-90) REVERT: A 523 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7856 (pt) REVERT: A 524 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8183 (t) REVERT: A 581 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7891 (tpp80) outliers start: 36 outliers final: 16 residues processed: 268 average time/residue: 0.2592 time to fit residues: 107.8183 Evaluate side-chains 272 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN C 124 GLN B 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17396 Z= 0.350 Angle : 0.550 8.097 23560 Z= 0.284 Chirality : 0.042 0.170 2628 Planarity : 0.004 0.049 2956 Dihedral : 6.811 131.331 2372 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.49 % Allowed : 13.61 % Favored : 83.90 % 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: 1.58 (0.19), residues: 2116 helix: 1.95 (0.14), residues: 1496 sheet: 0.10 (0.54), residues: 88 loop : -1.47 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 281 HIS 0.003 0.001 HIS D 392 PHE 0.021 0.001 PHE D 236 TYR 0.015 0.002 TYR D 411 ARG 0.003 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 1.808 Fit side-chains REVERT: D 218 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8593 (mp) REVERT: D 259 PHE cc_start: 0.8073 (m-80) cc_final: 0.7747 (m-80) REVERT: D 286 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7797 (t-90) REVERT: D 523 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7693 (pt) REVERT: D 524 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8180 (t) REVERT: D 581 ARG cc_start: 0.8373 (ttp80) cc_final: 0.7921 (tpp80) REVERT: C 218 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 259 PHE cc_start: 0.8072 (m-80) cc_final: 0.7747 (m-80) REVERT: C 286 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7795 (t-90) REVERT: C 523 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7692 (pt) REVERT: C 524 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8182 (t) REVERT: C 581 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7921 (tpp80) REVERT: B 218 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 259 PHE cc_start: 0.8073 (m-80) cc_final: 0.7748 (m-80) REVERT: B 286 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: B 523 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7693 (pt) REVERT: B 524 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 581 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7920 (tpp80) REVERT: A 218 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 259 PHE cc_start: 0.8074 (m-80) cc_final: 0.7750 (m-80) REVERT: A 286 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: A 523 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7693 (pt) REVERT: A 524 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8181 (t) REVERT: A 581 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7921 (tpp80) outliers start: 44 outliers final: 20 residues processed: 268 average time/residue: 0.2560 time to fit residues: 106.6646 Evaluate side-chains 253 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17396 Z= 0.179 Angle : 0.508 7.820 23560 Z= 0.257 Chirality : 0.039 0.196 2628 Planarity : 0.003 0.042 2956 Dihedral : 6.819 132.246 2372 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.72 % Allowed : 14.23 % Favored : 83.05 % 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: 1.83 (0.19), residues: 2116 helix: 2.14 (0.14), residues: 1500 sheet: 0.05 (0.55), residues: 88 loop : -1.35 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 133 HIS 0.003 0.001 HIS D 421 PHE 0.023 0.001 PHE D 236 TYR 0.013 0.001 TYR C 411 ARG 0.001 0.000 ARG C 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 2.062 Fit side-chains REVERT: D 112 ARG cc_start: 0.7755 (mtp180) cc_final: 0.7449 (mtp180) REVERT: D 218 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8397 (mp) REVERT: D 259 PHE cc_start: 0.8046 (m-80) cc_final: 0.7711 (m-80) REVERT: D 286 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7645 (t-90) REVERT: D 523 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7708 (pt) REVERT: D 524 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8178 (t) REVERT: D 581 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7917 (tpp80) REVERT: C 112 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7437 (mtp180) REVERT: C 218 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8395 (mp) REVERT: C 259 PHE cc_start: 0.8046 (m-80) cc_final: 0.7712 (m-80) REVERT: C 286 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: C 523 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7706 (pt) REVERT: C 524 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8178 (t) REVERT: C 581 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7918 (tpp80) REVERT: B 112 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7435 (mtp180) REVERT: B 218 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 259 PHE cc_start: 0.8045 (m-80) cc_final: 0.7712 (m-80) REVERT: B 286 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: B 523 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7708 (pt) REVERT: B 524 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.8179 (t) REVERT: B 581 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7916 (tpp80) REVERT: A 112 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7393 (mtp180) REVERT: A 218 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8398 (mp) REVERT: A 259 PHE cc_start: 0.8047 (m-80) cc_final: 0.7715 (m-80) REVERT: A 286 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7644 (t-90) REVERT: A 523 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7709 (pt) REVERT: A 524 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8177 (t) REVERT: A 581 ARG cc_start: 0.8343 (ttp80) cc_final: 0.7916 (tpp80) outliers start: 48 outliers final: 20 residues processed: 260 average time/residue: 0.2705 time to fit residues: 108.5949 Evaluate side-chains 260 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17396 Z= 0.200 Angle : 0.507 7.822 23560 Z= 0.255 Chirality : 0.039 0.181 2628 Planarity : 0.003 0.044 2956 Dihedral : 6.784 132.098 2372 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.89 % Allowed : 13.95 % Favored : 83.16 % 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: 1.87 (0.19), residues: 2116 helix: 2.17 (0.14), residues: 1504 sheet: 0.07 (0.55), residues: 88 loop : -1.37 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 133 HIS 0.003 0.001 HIS C 421 PHE 0.022 0.001 PHE D 236 TYR 0.013 0.001 TYR D 411 ARG 0.001 0.000 ARG B 428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 232 time to evaluate : 1.984 Fit side-chains REVERT: D 259 PHE cc_start: 0.8047 (m-80) cc_final: 0.7707 (m-80) REVERT: D 286 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7618 (t-90) REVERT: D 523 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7818 (pt) REVERT: D 524 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (t) REVERT: D 581 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7973 (tpp80) REVERT: C 259 PHE cc_start: 0.8046 (m-80) cc_final: 0.7708 (m-80) REVERT: C 286 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7618 (t-90) REVERT: C 523 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 524 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8187 (t) REVERT: C 581 ARG cc_start: 0.8407 (ttp80) cc_final: 0.7975 (tpp80) REVERT: B 259 PHE cc_start: 0.8046 (m-80) cc_final: 0.7708 (m-80) REVERT: B 286 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7615 (t-90) REVERT: B 523 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7817 (pt) REVERT: B 524 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8188 (t) REVERT: B 581 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7974 (tpp80) REVERT: A 112 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7539 (mtp180) REVERT: A 259 PHE cc_start: 0.8047 (m-80) cc_final: 0.7709 (m-80) REVERT: A 286 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7615 (t-90) REVERT: A 523 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7820 (pt) REVERT: A 524 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8190 (t) REVERT: A 581 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7974 (tpp80) outliers start: 51 outliers final: 27 residues processed: 268 average time/residue: 0.2670 time to fit residues: 111.3365 Evaluate side-chains 271 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17396 Z= 0.184 Angle : 0.531 7.962 23560 Z= 0.268 Chirality : 0.039 0.203 2628 Planarity : 0.003 0.048 2956 Dihedral : 6.801 132.268 2372 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.66 % Allowed : 14.40 % Favored : 82.94 % 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: 1.92 (0.19), residues: 2116 helix: 2.24 (0.14), residues: 1496 sheet: 0.07 (0.55), residues: 88 loop : -1.43 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 133 HIS 0.003 0.001 HIS B 421 PHE 0.020 0.001 PHE B 236 TYR 0.012 0.001 TYR B 411 ARG 0.001 0.000 ARG D 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 233 time to evaluate : 1.910 Fit side-chains REVERT: D 113 MET cc_start: 0.8471 (mmm) cc_final: 0.8242 (mmm) REVERT: D 218 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8269 (mp) REVERT: D 259 PHE cc_start: 0.8038 (m-80) cc_final: 0.7697 (m-80) REVERT: D 286 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (t-90) REVERT: D 473 MET cc_start: 0.7644 (mmm) cc_final: 0.7360 (mmm) REVERT: D 523 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7854 (pt) REVERT: D 524 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8185 (t) REVERT: D 581 ARG cc_start: 0.8403 (ttp80) cc_final: 0.7970 (tpp80) REVERT: C 113 MET cc_start: 0.8471 (mmm) cc_final: 0.8242 (mmm) REVERT: C 218 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8267 (mp) REVERT: C 259 PHE cc_start: 0.8039 (m-80) cc_final: 0.7699 (m-80) REVERT: C 286 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: C 473 MET cc_start: 0.7646 (mmm) cc_final: 0.7366 (mmm) REVERT: C 523 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7853 (pt) REVERT: C 524 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8186 (t) REVERT: C 581 ARG cc_start: 0.8406 (ttp80) cc_final: 0.7972 (tpp80) REVERT: B 113 MET cc_start: 0.8472 (mmm) cc_final: 0.8241 (mmm) REVERT: B 218 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 259 PHE cc_start: 0.8040 (m-80) cc_final: 0.7700 (m-80) REVERT: B 286 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (t-90) REVERT: B 473 MET cc_start: 0.7649 (mmm) cc_final: 0.7367 (mmm) REVERT: B 523 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7854 (pt) REVERT: B 524 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8184 (t) REVERT: B 581 ARG cc_start: 0.8405 (ttp80) cc_final: 0.7970 (tpp80) REVERT: A 113 MET cc_start: 0.8463 (mmm) cc_final: 0.8257 (mmm) REVERT: A 218 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 259 PHE cc_start: 0.8041 (m-80) cc_final: 0.7702 (m-80) REVERT: A 286 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7612 (t-90) REVERT: A 473 MET cc_start: 0.7645 (mmm) cc_final: 0.7361 (mmm) REVERT: A 523 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7854 (pt) REVERT: A 524 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8188 (t) REVERT: A 581 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7969 (tpp80) outliers start: 47 outliers final: 24 residues processed: 269 average time/residue: 0.2648 time to fit residues: 111.4129 Evaluate side-chains 272 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17396 Z= 0.247 Angle : 0.553 7.838 23560 Z= 0.280 Chirality : 0.041 0.204 2628 Planarity : 0.004 0.052 2956 Dihedral : 6.809 131.931 2372 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.32 % Allowed : 14.74 % Favored : 82.94 % 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: 1.84 (0.19), residues: 2116 helix: 2.14 (0.14), residues: 1504 sheet: 0.06 (0.55), residues: 88 loop : -1.40 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 133 HIS 0.003 0.001 HIS C 421 PHE 0.020 0.001 PHE A 236 TYR 0.013 0.001 TYR C 411 ARG 0.001 0.000 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 1.835 Fit side-chains REVERT: D 218 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8350 (mp) REVERT: D 259 PHE cc_start: 0.8046 (m-80) cc_final: 0.7704 (m-80) REVERT: D 286 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: D 523 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7838 (pt) REVERT: D 524 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8196 (t) REVERT: D 581 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7975 (tpp80) REVERT: C 218 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 259 PHE cc_start: 0.8049 (m-80) cc_final: 0.7707 (m-80) REVERT: C 286 HIS cc_start: 0.8076 (OUTLIER) cc_final: 0.7665 (t-90) REVERT: C 523 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7841 (pt) REVERT: C 524 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8199 (t) REVERT: C 581 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7978 (tpp80) REVERT: B 218 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8349 (mp) REVERT: B 259 PHE cc_start: 0.8049 (m-80) cc_final: 0.7708 (m-80) REVERT: B 286 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: B 523 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7837 (pt) REVERT: B 524 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8196 (t) REVERT: B 581 ARG cc_start: 0.8410 (ttp80) cc_final: 0.7977 (tpp80) REVERT: A 113 MET cc_start: 0.8454 (mmm) cc_final: 0.8244 (mmm) REVERT: A 218 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 259 PHE cc_start: 0.8050 (m-80) cc_final: 0.7711 (m-80) REVERT: A 286 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7661 (t-90) REVERT: A 523 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7838 (pt) REVERT: A 524 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 581 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7975 (tpp80) outliers start: 41 outliers final: 24 residues processed: 256 average time/residue: 0.2606 time to fit residues: 103.8340 Evaluate side-chains 264 residues out of total 1928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 524 THR Chi-restraints excluded: chain D residue 534 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 523 ILE Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.168108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.120391 restraints weight = 20133.287| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.25 r_work: 0.3312 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17396 Z= 0.233 Angle : 0.545 7.817 23560 Z= 0.277 Chirality : 0.040 0.195 2628 Planarity : 0.004 0.054 2956 Dihedral : 6.822 131.960 2372 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.49 % Allowed : 14.57 % Favored : 82.94 % 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: 1.84 (0.19), residues: 2116 helix: 2.15 (0.14), residues: 1504 sheet: 0.06 (0.55), residues: 88 loop : -1.40 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 133 HIS 0.003 0.001 HIS B 421 PHE 0.026 0.001 PHE A 236 TYR 0.013 0.001 TYR A 411 ARG 0.001 0.000 ARG D 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.69 seconds wall clock time: 64 minutes 34.80 seconds (3874.80 seconds total)