Starting phenix.real_space_refine on Sun Aug 24 10:13:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3z_44161/08_2025/9b3z_44161.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 B 4 2.79 5 C 12592 2.51 5 N 3204 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19180 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4724 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 576} Chain breaks: 4 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'TRP:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'FZ4': 1, 'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.55, per 1000 atoms: 0.24 Number of scatterers: 19180 At special positions: 0 Unit cell: (131.97, 131.97, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 4 15.00 O 3260 8.00 N 3204 7.00 C 12592 6.00 B 4 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 825.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 66.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 92 through 103 removed outlier: 4.490A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.527A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.663A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 459 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.628A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.835A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.616A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 removed outlier: 3.998A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.490A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.527A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.662A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Proline residue: B 325 - end of helix Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 459 Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 3.616A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 650 removed outlier: 3.999A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.489A pdb=" N LEU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.526A pdb=" N LEU C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 262 through 282 removed outlier: 3.672A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.663A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 4.964A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 459 Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 3.617A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.913A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 650 removed outlier: 3.998A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 673 removed outlier: 4.001A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 88 through 91 Processing helix chain 'D' and resid 92 through 103 removed outlier: 4.489A pdb=" N LEU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.526A pdb=" N LEU D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.504A pdb=" N ASP D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 removed outlier: 3.548A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 262 through 282 removed outlier: 3.673A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.667A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.662A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.237A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Proline residue: D 325 - end of helix Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.656A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 413 removed outlier: 4.965A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 459 Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.629A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.836A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.608A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 3.615A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 removed outlier: 3.914A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 650 removed outlier: 3.999A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 673 removed outlier: 4.002A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.908A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3084 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: 3.45 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3249 1.33 - 1.45: 5281 1.45 - 1.57: 10902 1.57 - 1.69: 24 1.69 - 1.81: 176 Bond restraints: 19632 Sorted by residual: bond pdb=" C17 RTO D 803 " pdb=" O19 RTO D 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO B 803 " pdb=" O19 RTO B 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO A 803 " pdb=" O19 RTO A 803 " ideal model delta sigma weight residual 1.256 1.346 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C17 RTO C 803 " pdb=" O19 RTO C 803 " ideal model delta sigma weight residual 1.256 1.344 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C14 RTO B 803 " pdb=" C17 RTO B 803 " ideal model delta sigma weight residual 1.531 1.473 0.058 2.00e-02 2.50e+03 8.41e+00 ... (remaining 19627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 25970 1.43 - 2.85: 448 2.85 - 4.28: 130 4.28 - 5.70: 41 5.70 - 7.13: 23 Bond angle restraints: 26612 Sorted by residual: angle pdb=" CA PRO C 261 " pdb=" N PRO C 261 " pdb=" CD PRO C 261 " ideal model delta sigma weight residual 112.00 105.07 6.93 1.40e+00 5.10e-01 2.45e+01 angle pdb=" CA PRO A 261 " pdb=" N PRO A 261 " pdb=" CD PRO A 261 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" CD PRO B 261 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA PRO D 261 " pdb=" N PRO D 261 " pdb=" CD PRO D 261 " ideal model delta sigma weight residual 112.00 105.13 6.87 1.40e+00 5.10e-01 2.41e+01 angle pdb=" C PHE A 618 " pdb=" N ARG A 619 " pdb=" CA ARG A 619 " ideal model delta sigma weight residual 120.38 124.87 -4.49 1.37e+00 5.33e-01 1.07e+01 ... (remaining 26607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 10652 23.01 - 46.02: 740 46.02 - 69.03: 144 69.03 - 92.04: 24 92.04 - 115.06: 8 Dihedral angle restraints: 11568 sinusoidal: 4620 harmonic: 6948 Sorted by residual: dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N GLY A 210 " pdb=" CA GLY A 210 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 11565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2248 0.036 - 0.073: 617 0.073 - 0.109: 133 0.109 - 0.146: 14 0.146 - 0.182: 8 Chirality restraints: 3020 Sorted by residual: chirality pdb=" CA PRO B 261 " pdb=" N PRO B 261 " pdb=" C PRO B 261 " pdb=" CB PRO B 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PRO D 261 " pdb=" N PRO D 261 " pdb=" C PRO D 261 " pdb=" CB PRO D 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CA PRO C 261 " pdb=" N PRO C 261 " pdb=" C PRO C 261 " pdb=" CB PRO C 261 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 3017 not shown) Planarity restraints: 3256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 260 " -0.061 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO C 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 261 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " -0.061 5.00e-02 4.00e+02 8.81e-02 1.24e+01 pdb=" N PRO B 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 260 " -0.061 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 261 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.049 5.00e-02 4.00e+02 ... (remaining 3253 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5183 2.80 - 3.33: 18291 3.33 - 3.85: 31590 3.85 - 4.38: 38597 4.38 - 4.90: 65971 Nonbonded interactions: 159632 Sorted by model distance: nonbonded pdb=" ND2 ASN A 263 " pdb=" OE2 GLU D 716 " model vdw 2.279 3.120 nonbonded pdb=" OE2 GLU A 716 " pdb=" ND2 ASN B 263 " model vdw 2.289 3.120 nonbonded pdb=" OE2 GLU C 716 " pdb=" ND2 ASN D 263 " model vdw 2.309 3.120 nonbonded pdb=" OE2 GLU B 716 " pdb=" ND2 ASN C 263 " model vdw 2.309 3.120 nonbonded pdb=" OH TYR C 544 " pdb=" OH TYR C 629 " model vdw 2.320 3.040 ... (remaining 159627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 19632 Z= 0.147 Angle : 0.562 7.129 26612 Z= 0.312 Chirality : 0.036 0.182 3020 Planarity : 0.004 0.088 3256 Dihedral : 16.148 115.056 7072 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.87 % Allowed : 16.36 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.17), residues: 2336 helix: 0.34 (0.13), residues: 1400 sheet: -0.21 (0.50), residues: 112 loop : 0.02 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.022 0.001 TYR D 228 PHE 0.009 0.001 PHE C 547 TRP 0.014 0.001 TRP B 333 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00319 (19632) covalent geometry : angle 0.56188 (26612) hydrogen bonds : bond 0.25155 ( 1068) hydrogen bonds : angle 6.61413 ( 3084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 637 LEU cc_start: 0.7702 (mm) cc_final: 0.7440 (mt) REVERT: B 496 TRP cc_start: 0.7136 (m100) cc_final: 0.6914 (m100) REVERT: C 496 TRP cc_start: 0.7130 (m100) cc_final: 0.6926 (m100) REVERT: C 637 LEU cc_start: 0.7707 (mm) cc_final: 0.7440 (mt) REVERT: D 496 TRP cc_start: 0.7122 (m100) cc_final: 0.6912 (m100) REVERT: D 637 LEU cc_start: 0.7717 (mm) cc_final: 0.7427 (mt) outliers start: 37 outliers final: 20 residues processed: 329 average time/residue: 0.4867 time to fit residues: 186.7087 Evaluate side-chains 285 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 235 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 247 ASN A 313 HIS A 316 GLN A 370 HIS A 639 ASN B 165 HIS B 247 ASN B 313 HIS B 316 GLN B 370 HIS B 639 ASN C 165 HIS C 247 ASN C 313 HIS C 370 HIS C 639 ASN D 165 HIS D 247 ASN D 313 HIS D 316 GLN D 363 HIS D 370 HIS D 639 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.175061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136794 restraints weight = 22324.969| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.08 r_work: 0.3432 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 19632 Z= 0.296 Angle : 0.648 5.912 26612 Z= 0.324 Chirality : 0.043 0.140 3020 Planarity : 0.005 0.040 3256 Dihedral : 10.253 122.744 2844 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.80 % Allowed : 13.59 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2336 helix: 1.12 (0.13), residues: 1452 sheet: -0.38 (0.61), residues: 84 loop : 0.27 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 392 TYR 0.015 0.002 TYR A 403 PHE 0.019 0.002 PHE B 547 TRP 0.022 0.002 TRP A 333 HIS 0.008 0.002 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00720 (19632) covalent geometry : angle 0.64809 (26612) hydrogen bonds : bond 0.05349 ( 1068) hydrogen bonds : angle 4.04601 ( 3084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 301 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 457 TRP cc_start: 0.7562 (t60) cc_final: 0.7247 (t60) REVERT: A 637 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7425 (mt) REVERT: B 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (mp) REVERT: B 457 TRP cc_start: 0.7557 (t60) cc_final: 0.7244 (t60) REVERT: B 637 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7415 (mt) REVERT: C 448 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8518 (mp) REVERT: C 457 TRP cc_start: 0.7591 (t60) cc_final: 0.7270 (t60) REVERT: C 637 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7446 (mt) REVERT: D 448 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 457 TRP cc_start: 0.7575 (t60) cc_final: 0.7264 (t60) REVERT: D 637 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7417 (mt) REVERT: D 709 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7779 (pt0) outliers start: 95 outliers final: 37 residues processed: 357 average time/residue: 0.4881 time to fit residues: 203.1685 Evaluate side-chains 324 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 231 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 1 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 414 GLN A 487 GLN B 247 ASN B 414 GLN B 487 GLN C 247 ASN C 414 GLN C 487 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN D 487 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142062 restraints weight = 22484.298| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.07 r_work: 0.3524 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19632 Z= 0.101 Angle : 0.467 5.280 26612 Z= 0.237 Chirality : 0.037 0.161 3020 Planarity : 0.004 0.038 3256 Dihedral : 8.730 94.030 2824 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.08 % Allowed : 17.17 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.18), residues: 2336 helix: 1.82 (0.13), residues: 1448 sheet: 0.04 (0.52), residues: 112 loop : 0.35 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 458 TYR 0.015 0.001 TYR C 228 PHE 0.013 0.001 PHE C 547 TRP 0.015 0.001 TRP D 333 HIS 0.003 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00225 (19632) covalent geometry : angle 0.46677 (26612) hydrogen bonds : bond 0.03344 ( 1068) hydrogen bonds : angle 3.51423 ( 3084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 302 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6826 (tp) REVERT: A 448 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8513 (mp) REVERT: A 637 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7402 (mt) REVERT: B 448 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 637 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7401 (mt) REVERT: C 448 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 637 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7412 (mt) REVERT: D 448 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 637 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7433 (mt) outliers start: 61 outliers final: 26 residues processed: 341 average time/residue: 0.4177 time to fit residues: 166.8075 Evaluate side-chains 306 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 93 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 233 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 222 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.178870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140621 restraints weight = 22448.967| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.05 r_work: 0.3497 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19632 Z= 0.130 Angle : 0.489 8.738 26612 Z= 0.241 Chirality : 0.038 0.194 3020 Planarity : 0.003 0.039 3256 Dihedral : 8.648 95.522 2824 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.59 % Allowed : 16.92 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.18), residues: 2336 helix: 1.89 (0.13), residues: 1452 sheet: 0.05 (0.53), residues: 112 loop : 0.33 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 459 TYR 0.015 0.001 TYR B 228 PHE 0.013 0.001 PHE D 547 TRP 0.015 0.001 TRP B 333 HIS 0.004 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00309 (19632) covalent geometry : angle 0.48928 (26612) hydrogen bonds : bond 0.03356 ( 1068) hydrogen bonds : angle 3.47752 ( 3084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 637 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 448 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 637 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7397 (mt) REVERT: C 448 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8544 (mp) REVERT: C 637 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7443 (mt) REVERT: D 448 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8550 (mp) REVERT: D 637 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7451 (mt) outliers start: 71 outliers final: 40 residues processed: 327 average time/residue: 0.4443 time to fit residues: 170.7931 Evaluate side-chains 312 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 46 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 202 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN C 452 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142260 restraints weight = 22428.219| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.08 r_work: 0.3522 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 19632 Z= 0.105 Angle : 0.478 9.654 26612 Z= 0.233 Chirality : 0.037 0.180 3020 Planarity : 0.003 0.040 3256 Dihedral : 8.263 84.911 2824 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.03 % Allowed : 18.48 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.18), residues: 2336 helix: 2.05 (0.14), residues: 1452 sheet: 0.03 (0.51), residues: 112 loop : 0.36 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 458 TYR 0.014 0.001 TYR D 228 PHE 0.010 0.001 PHE C 547 TRP 0.014 0.001 TRP A 333 HIS 0.003 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00241 (19632) covalent geometry : angle 0.47828 (26612) hydrogen bonds : bond 0.03064 ( 1068) hydrogen bonds : angle 3.33718 ( 3084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.7021 (mp) cc_final: 0.6685 (mt) REVERT: A 448 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8483 (mp) REVERT: A 637 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 106 LEU cc_start: 0.7018 (mp) cc_final: 0.6657 (mt) REVERT: B 435 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6914 (tp) REVERT: B 448 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8557 (mp) REVERT: B 637 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7386 (mt) REVERT: C 106 LEU cc_start: 0.6986 (mp) cc_final: 0.6643 (mt) REVERT: C 448 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8484 (mp) REVERT: C 539 ARG cc_start: 0.8797 (mpp80) cc_final: 0.8593 (tpp80) REVERT: C 637 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7412 (mt) REVERT: D 106 LEU cc_start: 0.7017 (mp) cc_final: 0.6679 (mt) REVERT: D 448 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 536 ASP cc_start: 0.7259 (t70) cc_final: 0.6794 (m-30) REVERT: D 637 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7423 (mt) outliers start: 60 outliers final: 31 residues processed: 317 average time/residue: 0.4530 time to fit residues: 169.1348 Evaluate side-chains 304 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 83 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 230 optimal weight: 0.0670 chunk 103 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 0.0050 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN D 247 ASN D 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.182915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145931 restraints weight = 22383.893| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.10 r_work: 0.3556 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 19632 Z= 0.082 Angle : 0.454 9.857 26612 Z= 0.220 Chirality : 0.036 0.158 3020 Planarity : 0.003 0.038 3256 Dihedral : 8.005 66.040 2824 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 19.29 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.18), residues: 2336 helix: 2.23 (0.14), residues: 1460 sheet: 0.11 (0.49), residues: 112 loop : 0.36 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 539 TYR 0.018 0.001 TYR B 228 PHE 0.007 0.001 PHE C 311 TRP 0.013 0.001 TRP B 333 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00174 (19632) covalent geometry : angle 0.45444 (26612) hydrogen bonds : bond 0.02787 ( 1068) hydrogen bonds : angle 3.18766 ( 3084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.6977 (mp) cc_final: 0.6513 (mt) REVERT: A 139 LEU cc_start: 0.7823 (tp) cc_final: 0.7531 (mt) REVERT: A 539 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8154 (mpp80) REVERT: A 637 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7400 (mt) REVERT: B 106 LEU cc_start: 0.6969 (mp) cc_final: 0.6502 (mt) REVERT: B 139 LEU cc_start: 0.7830 (tp) cc_final: 0.7542 (mt) REVERT: B 433 MET cc_start: 0.7744 (tpp) cc_final: 0.7439 (mmm) REVERT: B 435 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6862 (tp) REVERT: B 448 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8515 (mp) REVERT: B 539 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8067 (mpp80) REVERT: B 637 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7391 (mt) REVERT: C 106 LEU cc_start: 0.6975 (mp) cc_final: 0.6513 (mt) REVERT: C 139 LEU cc_start: 0.7826 (tp) cc_final: 0.7540 (mt) REVERT: C 433 MET cc_start: 0.7676 (tpp) cc_final: 0.6182 (tpt) REVERT: C 637 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7401 (mt) REVERT: D 106 LEU cc_start: 0.6977 (mp) cc_final: 0.6526 (mt) REVERT: D 139 LEU cc_start: 0.7822 (tp) cc_final: 0.7535 (mt) REVERT: D 433 MET cc_start: 0.7704 (tpp) cc_final: 0.6184 (tpt) REVERT: D 448 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8487 (mp) REVERT: D 637 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7431 (mt) outliers start: 60 outliers final: 27 residues processed: 321 average time/residue: 0.4694 time to fit residues: 174.6659 Evaluate side-chains 293 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 148 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 173 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 192 optimal weight: 0.0870 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS B 269 HIS C 269 HIS D 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.183454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145994 restraints weight = 22410.726| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.06 r_work: 0.3576 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19632 Z= 0.082 Angle : 0.463 9.441 26612 Z= 0.224 Chirality : 0.037 0.200 3020 Planarity : 0.003 0.038 3256 Dihedral : 7.771 60.493 2824 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.22 % Allowed : 20.25 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.18), residues: 2336 helix: 2.24 (0.14), residues: 1464 sheet: 0.22 (0.48), residues: 112 loop : 0.27 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 617 TYR 0.016 0.001 TYR C 228 PHE 0.007 0.001 PHE B 311 TRP 0.010 0.001 TRP D 333 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00173 (19632) covalent geometry : angle 0.46284 (26612) hydrogen bonds : bond 0.02728 ( 1068) hydrogen bonds : angle 3.16678 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.7057 (mp) cc_final: 0.6547 (mt) REVERT: A 139 LEU cc_start: 0.7860 (tp) cc_final: 0.7559 (mt) REVERT: A 334 CYS cc_start: 0.7562 (t) cc_final: 0.7110 (t) REVERT: A 339 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7207 (ttm-80) REVERT: A 539 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8094 (mpp80) REVERT: A 637 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7406 (mt) REVERT: B 106 LEU cc_start: 0.7044 (mp) cc_final: 0.6543 (mt) REVERT: B 139 LEU cc_start: 0.7864 (tp) cc_final: 0.7586 (mt) REVERT: B 433 MET cc_start: 0.7747 (tpp) cc_final: 0.7510 (mmm) REVERT: B 448 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (mp) REVERT: B 539 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8055 (mpp80) REVERT: B 637 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7330 (mt) REVERT: C 106 LEU cc_start: 0.7004 (mp) cc_final: 0.6497 (mt) REVERT: C 139 LEU cc_start: 0.7861 (tp) cc_final: 0.7582 (mt) REVERT: C 334 CYS cc_start: 0.7573 (t) cc_final: 0.7122 (t) REVERT: C 339 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7219 (ttm-80) REVERT: C 637 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7370 (mt) REVERT: D 106 LEU cc_start: 0.7055 (mp) cc_final: 0.6559 (mt) REVERT: D 139 LEU cc_start: 0.7825 (tp) cc_final: 0.7557 (mt) REVERT: D 334 CYS cc_start: 0.7546 (t) cc_final: 0.7095 (t) REVERT: D 339 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7228 (ttm-80) REVERT: D 539 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8153 (mpp80) REVERT: D 637 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7423 (mt) outliers start: 44 outliers final: 27 residues processed: 304 average time/residue: 0.4402 time to fit residues: 155.6131 Evaluate side-chains 294 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 709 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 46 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 118 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.180211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.142186 restraints weight = 22427.444| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.01 r_work: 0.3521 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19632 Z= 0.125 Angle : 0.501 9.466 26612 Z= 0.241 Chirality : 0.037 0.178 3020 Planarity : 0.003 0.040 3256 Dihedral : 7.942 59.412 2824 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.13 % Allowed : 19.70 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.18), residues: 2336 helix: 2.18 (0.14), residues: 1452 sheet: 0.22 (0.49), residues: 112 loop : 0.32 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.017 0.001 TYR B 228 PHE 0.008 0.001 PHE D 705 TRP 0.010 0.001 TRP D 333 HIS 0.004 0.001 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00296 (19632) covalent geometry : angle 0.50106 (26612) hydrogen bonds : bond 0.03127 ( 1068) hydrogen bonds : angle 3.28955 ( 3084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.7037 (mp) cc_final: 0.6624 (mt) REVERT: A 539 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8233 (mpp80) REVERT: A 637 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7398 (mt) REVERT: B 106 LEU cc_start: 0.6979 (mp) cc_final: 0.6531 (mt) REVERT: B 334 CYS cc_start: 0.7587 (t) cc_final: 0.7179 (t) REVERT: B 339 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7343 (ttm-80) REVERT: B 433 MET cc_start: 0.7757 (tpp) cc_final: 0.7454 (mmm) REVERT: B 448 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 539 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8105 (mpp80) REVERT: B 637 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7389 (mt) REVERT: C 106 LEU cc_start: 0.7011 (mp) cc_final: 0.6593 (mt) REVERT: C 637 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 106 LEU cc_start: 0.7004 (mp) cc_final: 0.6571 (mt) REVERT: D 539 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8169 (mpp80) REVERT: D 637 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7435 (mt) outliers start: 62 outliers final: 41 residues processed: 312 average time/residue: 0.4081 time to fit residues: 149.2348 Evaluate side-chains 307 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 709 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 193 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN C 414 GLN D 247 ASN D 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139388 restraints weight = 22434.272| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.08 r_work: 0.3476 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19632 Z= 0.180 Angle : 0.555 9.625 26612 Z= 0.268 Chirality : 0.040 0.207 3020 Planarity : 0.004 0.040 3256 Dihedral : 8.144 67.193 2824 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.18 % Allowed : 20.35 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.18), residues: 2336 helix: 1.94 (0.14), residues: 1452 sheet: -0.05 (0.50), residues: 112 loop : 0.22 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 339 TYR 0.018 0.002 TYR B 228 PHE 0.012 0.001 PHE B 394 TRP 0.011 0.001 TRP B 333 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00437 (19632) covalent geometry : angle 0.55533 (26612) hydrogen bonds : bond 0.03532 ( 1068) hydrogen bonds : angle 3.47689 ( 3084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.6956 (mp) cc_final: 0.6504 (mt) REVERT: A 457 TRP cc_start: 0.7676 (t60) cc_final: 0.7261 (t60) REVERT: A 539 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8230 (mpp80) REVERT: A 637 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 106 LEU cc_start: 0.6960 (mp) cc_final: 0.6487 (mt) REVERT: B 448 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 457 TRP cc_start: 0.7618 (t60) cc_final: 0.7219 (t60) REVERT: B 539 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8142 (mpp80) REVERT: B 637 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7433 (mt) REVERT: B 645 MET cc_start: 0.8176 (mtm) cc_final: 0.7942 (mtt) REVERT: C 106 LEU cc_start: 0.6890 (mp) cc_final: 0.6416 (mt) REVERT: C 457 TRP cc_start: 0.7607 (t60) cc_final: 0.7209 (t60) REVERT: C 637 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7430 (mt) REVERT: D 106 LEU cc_start: 0.6936 (mp) cc_final: 0.6464 (mt) REVERT: D 457 TRP cc_start: 0.7685 (t60) cc_final: 0.7272 (t60) REVERT: D 539 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8251 (mpp80) REVERT: D 637 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7457 (mt) outliers start: 63 outliers final: 43 residues processed: 311 average time/residue: 0.4126 time to fit residues: 149.7601 Evaluate side-chains 324 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 358 GLU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 115 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 225 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.181029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141233 restraints weight = 22383.753| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.59 r_work: 0.3514 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19632 Z= 0.102 Angle : 0.500 9.839 26612 Z= 0.239 Chirality : 0.037 0.197 3020 Planarity : 0.003 0.040 3256 Dihedral : 7.526 61.181 2824 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.27 % Allowed : 20.71 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.18), residues: 2336 helix: 2.15 (0.14), residues: 1452 sheet: 0.00 (0.49), residues: 112 loop : 0.35 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.013 0.001 TYR D 412 PHE 0.015 0.001 PHE C 547 TRP 0.014 0.001 TRP C 333 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00235 (19632) covalent geometry : angle 0.49993 (26612) hydrogen bonds : bond 0.02940 ( 1068) hydrogen bonds : angle 3.33845 ( 3084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.6813 (mp) cc_final: 0.6275 (mt) REVERT: A 139 LEU cc_start: 0.7759 (tp) cc_final: 0.7484 (mt) REVERT: A 539 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8199 (mpp80) REVERT: A 637 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (mt) REVERT: B 106 LEU cc_start: 0.6807 (mp) cc_final: 0.6271 (mt) REVERT: B 334 CYS cc_start: 0.7619 (t) cc_final: 0.7192 (t) REVERT: B 339 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7378 (ttm-80) REVERT: B 448 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 490 ARG cc_start: 0.6797 (ttp-170) cc_final: 0.6513 (ttp-170) REVERT: B 539 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8113 (mpp80) REVERT: B 637 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7369 (mt) REVERT: C 106 LEU cc_start: 0.6800 (mp) cc_final: 0.6300 (mt) REVERT: C 637 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7366 (mt) REVERT: D 106 LEU cc_start: 0.6782 (mp) cc_final: 0.6269 (mt) REVERT: D 539 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8178 (mpp80) REVERT: D 637 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7375 (mt) outliers start: 45 outliers final: 34 residues processed: 307 average time/residue: 0.4046 time to fit residues: 144.8468 Evaluate side-chains 304 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 262 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 471 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 ARG Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 471 TYR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 539 ARG Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 685 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 225 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 204 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 234 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141869 restraints weight = 22400.074| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.60 r_work: 0.3528 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19632 Z= 0.099 Angle : 0.505 9.715 26612 Z= 0.242 Chirality : 0.038 0.211 3020 Planarity : 0.003 0.040 3256 Dihedral : 7.398 61.853 2824 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.02 % Allowed : 21.41 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.18), residues: 2336 helix: 2.22 (0.14), residues: 1440 sheet: 0.01 (0.48), residues: 112 loop : 0.37 (0.24), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.014 0.001 TYR B 412 PHE 0.010 0.001 PHE D 547 TRP 0.022 0.001 TRP C 333 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00228 (19632) covalent geometry : angle 0.50541 (26612) hydrogen bonds : bond 0.02949 ( 1068) hydrogen bonds : angle 3.31930 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5212.49 seconds wall clock time: 90 minutes 7.05 seconds (5407.05 seconds total)