Starting phenix.real_space_refine on Sun Aug 4 15:35:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x5f_38068/08_2024/8x5f_38068_neut_trim.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 40 5.16 5 C 7212 2.51 5 N 1669 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10843 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5024 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5020 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 399 Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 10, 'POV:plan-1': 11} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 396 Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 9, 'POV:plan-1': 11} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.90, per 1000 atoms: 0.64 Number of scatterers: 10843 At special positions: 0 Unit cell: (111.35, 128.35, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 26 15.00 O 1896 8.00 N 1669 7.00 C 7212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.775A pdb=" N HIS A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.481A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 removed outlier: 3.514A pdb=" N PHE A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 53 through 103 removed outlier: 3.525A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 168 Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.633A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.728A pdb=" N GLN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.572A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.564A pdb=" N ARG A 236 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.935A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.535A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.825A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.568A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.105A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 3.515A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 475 through 502 removed outlier: 4.493A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.647A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 580 removed outlier: 3.816A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 620 removed outlier: 3.658A pdb=" N ILE A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.748A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.775A pdb=" N HIS B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.221A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.514A pdb=" N PHE B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.732A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 103 removed outlier: 3.525A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 168 removed outlier: 3.513A pdb=" N ARG B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.632A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.728A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.572A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 3.565A pdb=" N ARG B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.935A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.535A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.825A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.568A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.104A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 502 removed outlier: 4.494A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.647A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 removed outlier: 3.816A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 577 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 620 removed outlier: 3.658A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.748A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2043 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: 2.75 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1572 1.31 - 1.43: 3167 1.43 - 1.56: 6253 1.56 - 1.69: 47 1.69 - 1.82: 56 Bond restraints: 11095 Sorted by residual: bond pdb=" C31 POV A 713 " pdb=" O32 POV A 713 " ideal model delta sigma weight residual 1.206 1.402 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C31 POV A 711 " pdb=" O32 POV A 711 " ideal model delta sigma weight residual 1.206 1.401 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C31 POV A 717 " pdb=" O32 POV A 717 " ideal model delta sigma weight residual 1.206 1.400 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C31 POV B1110 " pdb=" O32 POV B1110 " ideal model delta sigma weight residual 1.206 1.399 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C31 POV B1112 " pdb=" O32 POV B1112 " ideal model delta sigma weight residual 1.206 1.398 -0.192 2.00e-02 2.50e+03 9.24e+01 ... (remaining 11090 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.39: 249 106.39 - 113.30: 6112 113.30 - 120.21: 4147 120.21 - 127.11: 4292 127.11 - 134.02: 127 Bond angle restraints: 14927 Sorted by residual: angle pdb=" C28 POV A 718 " pdb=" C29 POV A 718 " pdb="C210 POV A 718 " ideal model delta sigma weight residual 127.79 108.59 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" C29 POV A 718 " pdb="C210 POV A 718 " pdb="C211 POV A 718 " ideal model delta sigma weight residual 127.67 108.56 19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" C28 POV B1107 " pdb=" C29 POV B1107 " pdb="C210 POV B1107 " ideal model delta sigma weight residual 127.79 108.81 18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" N SER A 93 " pdb=" CA SER A 93 " pdb=" C SER A 93 " ideal model delta sigma weight residual 111.28 118.12 -6.84 1.09e+00 8.42e-01 3.94e+01 angle pdb=" N SER B 93 " pdb=" CA SER B 93 " pdb=" C SER B 93 " ideal model delta sigma weight residual 111.28 118.11 -6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 14922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 6376 31.27 - 62.53: 284 62.53 - 93.80: 30 93.80 - 125.07: 5 125.07 - 156.34: 4 Dihedral angle restraints: 6699 sinusoidal: 3053 harmonic: 3646 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 163.35 -70.35 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" C VAL B 626 " pdb=" N VAL B 626 " pdb=" CA VAL B 626 " pdb=" CB VAL B 626 " ideal model delta harmonic sigma weight residual -122.00 -135.65 13.65 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CA VAL B 626 " pdb=" CB VAL B 626 " ideal model delta harmonic sigma weight residual 123.40 135.07 -11.67 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 6696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1383 0.076 - 0.151: 152 0.151 - 0.227: 22 0.227 - 0.302: 12 0.302 - 0.378: 3 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA THR B 582 " pdb=" N THR B 582 " pdb=" C THR B 582 " pdb=" CB THR B 582 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA VAL B 626 " pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CB VAL B 626 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA HIS B 441 " pdb=" N HIS B 441 " pdb=" C HIS B 441 " pdb=" CB HIS B 441 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1569 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1107 " -0.152 2.00e-02 2.50e+03 2.51e-01 6.30e+02 pdb=" C29 POV B1107 " 0.321 2.00e-02 2.50e+03 pdb="C210 POV B1107 " -0.321 2.00e-02 2.50e+03 pdb="C211 POV B1107 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 718 " 0.141 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C29 POV A 718 " -0.277 2.00e-02 2.50e+03 pdb="C210 POV A 718 " 0.277 2.00e-02 2.50e+03 pdb="C211 POV A 718 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 35 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C GLN B 35 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN B 35 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 36 " -0.022 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 222 2.70 - 3.25: 10150 3.25 - 3.80: 16045 3.80 - 4.35: 20221 4.35 - 4.90: 35841 Nonbonded interactions: 82479 Sorted by model distance: nonbonded pdb=" N GLN A 227 " pdb=" OE1 GLN A 227 " model vdw 2.149 3.120 nonbonded pdb=" OG SER B 497 " pdb=" O THR B 582 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 217 " pdb=" NH1 ARG B 308 " model vdw 2.304 3.120 nonbonded pdb=" O ARG A 217 " pdb=" NH1 ARG A 308 " model vdw 2.305 3.120 nonbonded pdb=" OG SER A 497 " pdb=" O THR A 582 " model vdw 2.305 3.040 ... (remaining 82474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 441 or (resid 442 through 443 and (name N or nam \ e CA or name C or name O or name CB )) or resid 444 through 635 or resid 702 thr \ ough 704 or resid 707 or (resid 708 and (name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O31 or \ name O32 or name C310 or name C311)) or resid 710 or resid 712 through 716 or ( \ resid 719 and (name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 or \ name C311 or name C312 or name C313 or name C314)) or resid 720 or (resid 721 an \ d (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or name \ C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 1 through 635 or resid 1102 through 1104 or resid 1107 or \ (resid 1108 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 o \ r name C311)) or resid 1110 or resid 1112 or (resid 1113 and (name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name O31 or name O32 or name C310 or name C311 or name C312)) or resid \ 1114 through 1116 or resid 1119 or (resid 1120 and (name N or name C1 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or nam \ e C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ name C3 or name C31 or name C32 or name C33 or name O11 or name O12 or name O13 \ or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (re \ sid 1121 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )))) } 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=0.45 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: 2.520 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.840 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.011 0.196 11095 Z= 0.680 Angle : 1.270 19.201 14927 Z= 0.591 Chirality : 0.057 0.378 1572 Planarity : 0.009 0.251 1794 Dihedral : 17.296 156.336 4329 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 0.67 % Allowed : 2.12 % Favored : 97.21 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1220 helix: 2.14 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.005 0.001 HIS B 313 PHE 0.019 0.002 PHE B 571 TYR 0.035 0.002 TYR B 524 ARG 0.004 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.089 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 181 average time/residue: 1.2993 time to fit residues: 252.2047 Evaluate side-chains 97 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 499 HIS B 127 ASN B 452 GLN B 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11095 Z= 0.259 Angle : 0.573 7.138 14927 Z= 0.307 Chirality : 0.040 0.141 1572 Planarity : 0.005 0.045 1794 Dihedral : 15.404 139.120 2045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.18 % Allowed : 11.16 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1220 helix: 2.41 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 607 HIS 0.010 0.002 HIS B 441 PHE 0.015 0.002 PHE B 517 TYR 0.027 0.002 TYR B 524 ARG 0.006 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.196 Fit side-chains REVERT: B 468 ARG cc_start: 0.7626 (tmt170) cc_final: 0.7398 (tmt170) outliers start: 33 outliers final: 13 residues processed: 121 average time/residue: 1.3347 time to fit residues: 173.8730 Evaluate side-chains 100 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11095 Z= 0.278 Angle : 0.545 5.921 14927 Z= 0.294 Chirality : 0.040 0.140 1572 Planarity : 0.005 0.040 1794 Dihedral : 14.470 124.949 2044 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.72 % Rotamer: Outliers : 3.08 % Allowed : 12.61 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.25), residues: 1220 helix: 2.46 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.46 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 607 HIS 0.008 0.001 HIS B 441 PHE 0.017 0.002 PHE A 517 TYR 0.020 0.002 TYR A 524 ARG 0.007 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.170 Fit side-chains REVERT: A 159 ILE cc_start: 0.8307 (tp) cc_final: 0.8074 (tp) REVERT: A 167 LEU cc_start: 0.7495 (mp) cc_final: 0.7235 (tt) REVERT: B 159 ILE cc_start: 0.8246 (tp) cc_final: 0.7983 (tp) REVERT: B 167 LEU cc_start: 0.7477 (mp) cc_final: 0.7228 (tt) REVERT: B 529 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7341 (t0) REVERT: B 579 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7619 (mp) outliers start: 32 outliers final: 17 residues processed: 112 average time/residue: 1.1882 time to fit residues: 144.5630 Evaluate side-chains 106 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 499 HIS B 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11095 Z= 0.167 Angle : 0.454 5.752 14927 Z= 0.248 Chirality : 0.036 0.125 1572 Planarity : 0.004 0.038 1794 Dihedral : 13.494 111.395 2044 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.05 % Favored : 97.79 % Rotamer: Outliers : 1.92 % Allowed : 15.21 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.25), residues: 1220 helix: 2.77 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.29 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 607 HIS 0.008 0.001 HIS B 441 PHE 0.012 0.001 PHE B 517 TYR 0.010 0.001 TYR B 50 ARG 0.009 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.051 Fit side-chains REVERT: A 147 ASN cc_start: 0.8545 (m-40) cc_final: 0.8264 (m-40) REVERT: A 159 ILE cc_start: 0.8206 (tp) cc_final: 0.7984 (tp) REVERT: A 167 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6987 (tt) REVERT: B 147 ASN cc_start: 0.8532 (m-40) cc_final: 0.8272 (m-40) REVERT: B 159 ILE cc_start: 0.8181 (tp) cc_final: 0.7963 (tp) REVERT: B 167 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6975 (tt) outliers start: 20 outliers final: 7 residues processed: 105 average time/residue: 1.1435 time to fit residues: 130.7146 Evaluate side-chains 94 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 192 ASN A 540 ASN B 146 GLN B 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11095 Z= 0.271 Angle : 0.524 6.999 14927 Z= 0.282 Chirality : 0.039 0.131 1572 Planarity : 0.004 0.036 1794 Dihedral : 13.685 113.831 2040 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 3.46 % Allowed : 15.21 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1220 helix: 2.60 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 607 HIS 0.008 0.001 HIS B 441 PHE 0.017 0.002 PHE B 517 TYR 0.021 0.002 TYR B 496 ARG 0.006 0.001 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 91 time to evaluate : 1.234 Fit side-chains REVERT: A 159 ILE cc_start: 0.8261 (tp) cc_final: 0.8058 (tp) REVERT: A 167 LEU cc_start: 0.7304 (mp) cc_final: 0.7079 (tt) REVERT: B 159 ILE cc_start: 0.8258 (tp) cc_final: 0.8042 (tp) REVERT: B 167 LEU cc_start: 0.7347 (mp) cc_final: 0.7146 (tt) outliers start: 36 outliers final: 21 residues processed: 113 average time/residue: 1.1410 time to fit residues: 140.4684 Evaluate side-chains 107 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11095 Z= 0.253 Angle : 0.517 6.773 14927 Z= 0.278 Chirality : 0.038 0.128 1572 Planarity : 0.004 0.037 1794 Dihedral : 13.556 113.043 2040 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.30 % Rotamer: Outliers : 3.46 % Allowed : 15.40 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1220 helix: 2.61 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.42 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 607 HIS 0.008 0.001 HIS B 441 PHE 0.016 0.001 PHE B 517 TYR 0.025 0.002 TYR A 496 ARG 0.007 0.001 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 88 time to evaluate : 1.089 Fit side-chains REVERT: A 159 ILE cc_start: 0.8255 (tp) cc_final: 0.8038 (tp) REVERT: A 167 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7051 (tt) REVERT: A 540 ASN cc_start: 0.8365 (p0) cc_final: 0.8112 (p0) REVERT: B 159 ILE cc_start: 0.8256 (tp) cc_final: 0.8035 (tp) REVERT: B 167 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7169 (tt) outliers start: 36 outliers final: 22 residues processed: 111 average time/residue: 1.1578 time to fit residues: 140.0225 Evaluate side-chains 109 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11095 Z= 0.360 Angle : 0.598 7.312 14927 Z= 0.318 Chirality : 0.042 0.143 1572 Planarity : 0.005 0.039 1794 Dihedral : 14.147 115.883 2040 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.72 % Rotamer: Outliers : 3.27 % Allowed : 15.78 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1220 helix: 2.32 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 607 HIS 0.007 0.001 HIS B 441 PHE 0.020 0.002 PHE B 517 TYR 0.027 0.002 TYR B 496 ARG 0.005 0.001 ARG A 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.136 Fit side-chains REVERT: A 159 ILE cc_start: 0.8267 (tp) cc_final: 0.8051 (tp) REVERT: A 540 ASN cc_start: 0.8389 (p0) cc_final: 0.8117 (p0) REVERT: B 159 ILE cc_start: 0.8274 (tp) cc_final: 0.8052 (tp) outliers start: 34 outliers final: 27 residues processed: 112 average time/residue: 1.1695 time to fit residues: 142.3435 Evaluate side-chains 109 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11095 Z= 0.153 Angle : 0.490 8.202 14927 Z= 0.263 Chirality : 0.036 0.130 1572 Planarity : 0.004 0.037 1794 Dihedral : 13.076 109.879 2040 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.05 % Favored : 97.79 % Rotamer: Outliers : 1.83 % Allowed : 17.23 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.25), residues: 1220 helix: 2.73 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.007 0.001 HIS B 441 PHE 0.013 0.001 PHE A 460 TYR 0.025 0.001 TYR B 496 ARG 0.008 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.166 Fit side-chains REVERT: A 147 ASN cc_start: 0.8511 (m-40) cc_final: 0.8236 (m-40) REVERT: A 159 ILE cc_start: 0.8159 (tp) cc_final: 0.7948 (tp) REVERT: A 196 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6850 (m) REVERT: A 540 ASN cc_start: 0.8325 (p0) cc_final: 0.8107 (p0) REVERT: B 147 ASN cc_start: 0.8504 (m-40) cc_final: 0.8242 (m-40) REVERT: B 159 ILE cc_start: 0.8147 (tp) cc_final: 0.7924 (tp) REVERT: B 196 SER cc_start: 0.7122 (OUTLIER) cc_final: 0.6807 (m) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 1.1472 time to fit residues: 127.8309 Evaluate side-chains 96 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 0.0040 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11095 Z= 0.152 Angle : 0.476 9.862 14927 Z= 0.252 Chirality : 0.035 0.134 1572 Planarity : 0.004 0.039 1794 Dihedral : 12.179 110.899 2040 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.21 % Favored : 97.62 % Rotamer: Outliers : 1.44 % Allowed : 16.94 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.25), residues: 1220 helix: 3.04 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.23 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.006 0.001 HIS B 441 PHE 0.012 0.001 PHE B 460 TYR 0.026 0.001 TYR A 496 ARG 0.008 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8512 (m-40) cc_final: 0.8236 (m-40) REVERT: A 196 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6868 (m) REVERT: B 147 ASN cc_start: 0.8493 (m-40) cc_final: 0.8243 (m-40) REVERT: B 159 ILE cc_start: 0.8072 (tp) cc_final: 0.7867 (tp) REVERT: B 196 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6920 (m) outliers start: 15 outliers final: 11 residues processed: 103 average time/residue: 1.0213 time to fit residues: 115.3299 Evaluate side-chains 100 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 111 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 192 ASN A 310 ASN B 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11095 Z= 0.162 Angle : 0.502 9.022 14927 Z= 0.264 Chirality : 0.035 0.133 1572 Planarity : 0.004 0.039 1794 Dihedral : 12.056 110.522 2039 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.89 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 17.23 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.25), residues: 1220 helix: 3.10 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.006 0.001 HIS B 441 PHE 0.012 0.001 PHE A 460 TYR 0.025 0.001 TYR B 496 ARG 0.007 0.000 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.032 Fit side-chains REVERT: A 147 ASN cc_start: 0.8500 (m-40) cc_final: 0.8198 (m-40) REVERT: A 196 SER cc_start: 0.7153 (OUTLIER) cc_final: 0.6905 (m) REVERT: B 147 ASN cc_start: 0.8489 (m-40) cc_final: 0.8241 (m-40) REVERT: B 159 ILE cc_start: 0.7996 (tp) cc_final: 0.7791 (tp) REVERT: B 196 SER cc_start: 0.7129 (OUTLIER) cc_final: 0.6892 (m) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 1.0711 time to fit residues: 116.1486 Evaluate side-chains 98 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.172666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128577 restraints weight = 12613.440| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.13 r_work: 0.3312 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11095 Z= 0.185 Angle : 0.509 9.056 14927 Z= 0.269 Chirality : 0.036 0.138 1572 Planarity : 0.004 0.037 1794 Dihedral : 12.139 111.305 2039 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.21 % Favored : 97.62 % Rotamer: Outliers : 1.54 % Allowed : 17.32 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.25), residues: 1220 helix: 3.00 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 607 HIS 0.006 0.001 HIS B 441 PHE 0.012 0.001 PHE B 460 TYR 0.027 0.002 TYR B 496 ARG 0.007 0.000 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.87 seconds wall clock time: 62 minutes 31.09 seconds (3751.09 seconds total)