Starting phenix.real_space_refine on Thu Feb 15 19:58:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tkt_25981/02_2024/7tkt_25981_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 12 5.49 5 S 28 5.16 5 C 8844 2.51 5 N 2080 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 84": "OD1" <-> "OD2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "C ASP 84": "OD1" <-> "OD2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D GLU 274": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13252 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3103 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 23, 'TRANS': 366} Chain breaks: 1 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 210 Unusual residues: {'PGW': 13} Classifications: {'RNA': 1, 'undetermined': 13} Modifications used: {'rna3p': 1} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 552 Unresolved non-hydrogen dihedrals: 475 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 11, 'PGW:plan-2': 11, 'PGW:plan-3': 10} Unresolved non-hydrogen planarities: 104 Time building chain proxies: 7.62, per 1000 atoms: 0.58 Number of scatterers: 13252 At special positions: 0 Unit cell: (105.226, 105.226, 122.763, 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 28 16.00 P 12 15.00 O 2288 8.00 N 2080 7.00 C 8844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.13 Conformation dependent library (CDL) restraints added in 2.2 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 56.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 13 through 35 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 58 through 61 No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 103 through 125 removed outlier: 4.113A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 107 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 110 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 123 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 223 Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.555A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 294 removed outlier: 5.353A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.152A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.855A pdb=" N LEU A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 35 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 103 through 125 removed outlier: 4.113A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 107 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 110 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 125 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 223 Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.555A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 Processing helix chain 'B' and resid 272 through 275 No H-bonds generated for 'chain 'B' and resid 272 through 275' Processing helix chain 'B' and resid 281 through 294 removed outlier: 5.353A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.151A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.855A pdb=" N LEU B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 35 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 58 through 61 No H-bonds generated for 'chain 'C' and resid 58 through 61' Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 103 through 125 removed outlier: 4.113A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 107 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 110 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 123 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 223 Processing helix chain 'C' and resid 228 through 245 removed outlier: 3.555A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 Processing helix chain 'C' and resid 272 through 275 No H-bonds generated for 'chain 'C' and resid 272 through 275' Processing helix chain 'C' and resid 281 through 294 removed outlier: 5.353A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.152A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.855A pdb=" N LEU C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 35 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 58 through 61 No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 103 through 125 removed outlier: 4.113A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 107 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 110 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR D 123 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 223 Processing helix chain 'D' and resid 228 through 245 removed outlier: 3.555A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 281 through 294 removed outlier: 5.353A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.151A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.855A pdb=" N LEU D 414 " --> pdb=" O GLN D 410 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= B, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.761A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 360 removed outlier: 3.761A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= F, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.761A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= H, first strand: chain 'D' and resid 358 through 360 removed outlier: 3.760A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1704 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: 3.73 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3845 1.34 - 1.45: 1694 1.45 - 1.57: 7881 1.57 - 1.69: 16 1.69 - 1.81: 56 Bond restraints: 13492 Sorted by residual: bond pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.33e+01 bond pdb=" C10 PGW D 502 " pdb=" C9 PGW D 502 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 1.333 1.504 -0.171 2.00e-02 2.50e+03 7.29e+01 ... (remaining 13487 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.53: 735 107.53 - 114.68: 8061 114.68 - 121.84: 6937 121.84 - 129.00: 2323 129.00 - 136.15: 100 Bond angle restraints: 18156 Sorted by residual: angle pdb=" C10 PGW B 513 " pdb=" C9 PGW B 513 " pdb=" C8 PGW B 513 " ideal model delta sigma weight residual 127.02 105.95 21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW D 505 " pdb=" C9 PGW D 505 " pdb=" C8 PGW D 505 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 513 " pdb=" C9 PGW C 513 " pdb=" C8 PGW C 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " pdb=" C8 PGW A 513 " ideal model delta sigma weight residual 127.02 105.96 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " pdb=" C8 PGW C 510 " ideal model delta sigma weight residual 127.02 106.26 20.76 3.00e+00 1.11e-01 4.79e+01 ... (remaining 18151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 7972 34.68 - 69.36: 208 69.36 - 104.04: 52 104.04 - 138.71: 12 138.71 - 173.39: 32 Dihedral angle restraints: 8276 sinusoidal: 3688 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP C 501 " pdb=" O3' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.95 -160.95 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP D 507 " pdb=" O3' CMP D 507 " pdb=" P CMP D 507 " pdb=" O1P CMP D 507 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" C3' CMP A 501 " pdb=" O3' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 100.94 -160.94 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1311 0.034 - 0.069: 547 0.069 - 0.103: 191 0.103 - 0.137: 39 0.137 - 0.171: 12 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C02 PGW C 503 " pdb=" C01 PGW C 503 " pdb=" C03 PGW C 503 " pdb=" O01 PGW C 503 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" C02 PGW D 509 " pdb=" C01 PGW D 509 " pdb=" C03 PGW D 509 " pdb=" O01 PGW D 509 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA GLN D 412 " pdb=" N GLN D 412 " pdb=" C GLN D 412 " pdb=" CB GLN D 412 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 2097 not shown) Planarity restraints: 2172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 513 " -0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW B 513 " 0.161 2.00e-02 2.50e+03 pdb=" C8 PGW B 513 " -0.158 2.00e-02 2.50e+03 pdb=" C9 PGW B 513 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 505 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW D 505 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW D 505 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW D 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 513 " 0.159 2.00e-02 2.50e+03 1.59e-01 2.52e+02 pdb=" C10 PGW C 513 " -0.161 2.00e-02 2.50e+03 pdb=" C8 PGW C 513 " 0.158 2.00e-02 2.50e+03 pdb=" C9 PGW C 513 " -0.156 2.00e-02 2.50e+03 ... (remaining 2169 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1962 2.76 - 3.29: 12225 3.29 - 3.83: 21512 3.83 - 4.36: 22651 4.36 - 4.90: 40853 Nonbonded interactions: 99203 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.227 2.440 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR B 262 " pdb=" OD2 ASP B 388 " model vdw 2.264 2.440 ... (remaining 99198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'B' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'C' and (resid 10 through 416 or (resid 502 and (name C06 or name C07 or \ name C08 or name C09 or name C1 or name C10 or name C11 or name C12 or name C2 o \ r name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) o \ r resid 504 through 505 or resid 508 through 509 or (resid 510 through 511 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 513 \ through 514 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 \ )))) selection = (chain 'D' and (resid 10 through 416 or resid 502 or (resid 504 through 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 508 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or (resi \ d 509 and (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ 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 resid 510 through 511 or resid 513 through 514)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 4.350 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.280 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.171 13492 Z= 0.403 Angle : 1.255 21.069 18156 Z= 0.475 Chirality : 0.044 0.171 2100 Planarity : 0.008 0.159 2172 Dihedral : 21.053 173.393 5316 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1544 helix: 1.56 (0.18), residues: 936 sheet: 0.59 (0.57), residues: 84 loop : -1.78 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.002 0.001 HIS C 292 PHE 0.005 0.001 PHE D 386 TYR 0.009 0.001 TYR B 26 ARG 0.001 0.000 ARG D 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.543 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2560 time to fit residues: 56.8504 Evaluate side-chains 125 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13492 Z= 0.202 Angle : 0.613 8.911 18156 Z= 0.284 Chirality : 0.041 0.134 2100 Planarity : 0.004 0.039 2172 Dihedral : 20.850 162.446 2372 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.37 % Allowed : 9.10 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1544 helix: 1.85 (0.18), residues: 924 sheet: 0.30 (0.48), residues: 116 loop : -1.74 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS A 149 PHE 0.012 0.001 PHE D 40 TYR 0.016 0.001 TYR D 26 ARG 0.003 0.000 ARG D 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.375 Fit side-chains REVERT: A 82 LEU cc_start: 0.7406 (tt) cc_final: 0.6707 (mp) REVERT: B 82 LEU cc_start: 0.7399 (tt) cc_final: 0.6697 (mp) REVERT: C 82 LEU cc_start: 0.7403 (tt) cc_final: 0.6698 (mp) REVERT: D 82 LEU cc_start: 0.7404 (tt) cc_final: 0.6698 (mp) REVERT: D 369 MET cc_start: 0.7618 (tpp) cc_final: 0.7378 (tpt) outliers start: 5 outliers final: 0 residues processed: 126 average time/residue: 0.2298 time to fit residues: 43.9342 Evaluate side-chains 114 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.0010 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 0.0010 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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: 0.7997 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13492 Z= 0.159 Angle : 0.591 9.417 18156 Z= 0.270 Chirality : 0.040 0.135 2100 Planarity : 0.004 0.039 2172 Dihedral : 18.595 162.949 2372 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.90 % Allowed : 12.84 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1544 helix: 1.88 (0.18), residues: 924 sheet: 0.17 (0.47), residues: 116 loop : -1.69 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 176 HIS 0.001 0.000 HIS A 149 PHE 0.020 0.001 PHE B 40 TYR 0.011 0.001 TYR D 26 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.341 Fit side-chains REVERT: A 82 LEU cc_start: 0.7398 (tt) cc_final: 0.6731 (mp) REVERT: A 119 GLN cc_start: 0.6484 (tm-30) cc_final: 0.5906 (tt0) REVERT: B 82 LEU cc_start: 0.7395 (tt) cc_final: 0.6721 (mp) REVERT: B 119 GLN cc_start: 0.6528 (tm-30) cc_final: 0.5904 (tt0) REVERT: C 82 LEU cc_start: 0.7397 (tt) cc_final: 0.6727 (mp) REVERT: C 96 PHE cc_start: 0.6632 (m-10) cc_final: 0.6381 (m-10) REVERT: C 119 GLN cc_start: 0.6499 (tm-30) cc_final: 0.5869 (tt0) REVERT: D 82 LEU cc_start: 0.7400 (tt) cc_final: 0.6728 (mp) REVERT: D 96 PHE cc_start: 0.6580 (m-10) cc_final: 0.6334 (m-10) REVERT: D 119 GLN cc_start: 0.6499 (tm-30) cc_final: 0.5871 (tt0) outliers start: 12 outliers final: 0 residues processed: 135 average time/residue: 0.2346 time to fit residues: 48.1623 Evaluate side-chains 114 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.162 Angle : 0.592 9.659 18156 Z= 0.271 Chirality : 0.041 0.149 2100 Planarity : 0.004 0.038 2172 Dihedral : 17.294 163.031 2372 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.30 % Allowed : 17.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1544 helix: 1.89 (0.18), residues: 920 sheet: -0.09 (0.45), residues: 124 loop : -1.62 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.001 0.000 HIS D 149 PHE 0.038 0.001 PHE A 40 TYR 0.006 0.001 TYR C 26 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.498 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: A 82 LEU cc_start: 0.7426 (tt) cc_final: 0.6756 (mp) REVERT: A 119 GLN cc_start: 0.6496 (tm-30) cc_final: 0.5825 (tt0) REVERT: B 82 LEU cc_start: 0.7418 (tt) cc_final: 0.6759 (mp) REVERT: B 96 PHE cc_start: 0.6685 (m-80) cc_final: 0.6413 (m-10) REVERT: B 119 GLN cc_start: 0.6465 (tm-30) cc_final: 0.5775 (tt0) REVERT: C 82 LEU cc_start: 0.7419 (tt) cc_final: 0.6761 (mp) REVERT: C 96 PHE cc_start: 0.6692 (m-80) cc_final: 0.6420 (m-10) REVERT: C 119 GLN cc_start: 0.6456 (tm-30) cc_final: 0.6016 (tt0) REVERT: D 82 LEU cc_start: 0.7419 (tt) cc_final: 0.6761 (mp) REVERT: D 96 PHE cc_start: 0.6686 (m-80) cc_final: 0.6412 (m-10) REVERT: D 119 GLN cc_start: 0.6461 (tm-30) cc_final: 0.6017 (tt0) outliers start: 4 outliers final: 4 residues processed: 124 average time/residue: 0.2906 time to fit residues: 50.8449 Evaluate side-chains 124 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain D residue 26 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.2980 chunk 135 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8004 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13492 Z= 0.162 Angle : 0.577 10.413 18156 Z= 0.267 Chirality : 0.041 0.133 2100 Planarity : 0.004 0.037 2172 Dihedral : 16.662 163.307 2372 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.90 % Allowed : 17.69 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1544 helix: 1.90 (0.18), residues: 920 sheet: -0.12 (0.45), residues: 124 loop : -1.62 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.001 0.000 HIS C 149 PHE 0.041 0.001 PHE A 40 TYR 0.005 0.001 TYR D 175 ARG 0.009 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7433 (tt) cc_final: 0.6759 (mp) REVERT: A 119 GLN cc_start: 0.6551 (tm-30) cc_final: 0.6068 (tt0) REVERT: B 82 LEU cc_start: 0.7420 (tt) cc_final: 0.6767 (mp) REVERT: B 96 PHE cc_start: 0.6682 (m-80) cc_final: 0.6392 (m-10) REVERT: B 111 ARG cc_start: 0.6410 (ptm160) cc_final: 0.6198 (ptm160) REVERT: B 119 GLN cc_start: 0.6540 (tm-30) cc_final: 0.6075 (tt0) REVERT: C 82 LEU cc_start: 0.7425 (tt) cc_final: 0.6765 (mp) REVERT: C 96 PHE cc_start: 0.6798 (m-80) cc_final: 0.6524 (m-10) REVERT: C 119 GLN cc_start: 0.6538 (tm-30) cc_final: 0.5999 (tt0) REVERT: D 82 LEU cc_start: 0.7428 (tt) cc_final: 0.6769 (mp) REVERT: D 96 PHE cc_start: 0.6793 (m-80) cc_final: 0.6512 (m-10) REVERT: D 111 ARG cc_start: 0.6385 (ptm160) cc_final: 0.6159 (ptm160) REVERT: D 119 GLN cc_start: 0.6544 (tm-30) cc_final: 0.6009 (tt0) outliers start: 12 outliers final: 0 residues processed: 142 average time/residue: 0.2769 time to fit residues: 55.3773 Evaluate side-chains 117 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.0030 chunk 79 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13492 Z= 0.150 Angle : 0.585 9.958 18156 Z= 0.268 Chirality : 0.041 0.149 2100 Planarity : 0.004 0.036 2172 Dihedral : 16.297 163.172 2372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.82 % Allowed : 18.43 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1544 helix: 1.88 (0.18), residues: 920 sheet: -0.13 (0.45), residues: 124 loop : -1.64 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.001 0.000 HIS A 149 PHE 0.042 0.001 PHE A 40 TYR 0.010 0.001 TYR C 26 ARG 0.008 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7414 (tt) cc_final: 0.6792 (mp) REVERT: A 119 GLN cc_start: 0.6396 (tm-30) cc_final: 0.5918 (tt0) REVERT: B 82 LEU cc_start: 0.7419 (tt) cc_final: 0.6759 (mp) REVERT: B 119 GLN cc_start: 0.6386 (tm-30) cc_final: 0.5931 (tt0) REVERT: C 82 LEU cc_start: 0.7419 (tt) cc_final: 0.6763 (mp) REVERT: C 96 PHE cc_start: 0.6752 (m-80) cc_final: 0.6451 (m-10) REVERT: C 119 GLN cc_start: 0.6388 (tm-30) cc_final: 0.5866 (tt0) REVERT: D 82 LEU cc_start: 0.7422 (tt) cc_final: 0.6763 (mp) REVERT: D 119 GLN cc_start: 0.6379 (tm-30) cc_final: 0.5865 (tt0) outliers start: 11 outliers final: 0 residues processed: 138 average time/residue: 0.2658 time to fit residues: 53.1500 Evaluate side-chains 115 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13492 Z= 0.166 Angle : 0.603 11.453 18156 Z= 0.277 Chirality : 0.042 0.257 2100 Planarity : 0.004 0.035 2172 Dihedral : 16.113 163.478 2372 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.30 % Allowed : 20.07 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1544 helix: 2.06 (0.18), residues: 896 sheet: -0.16 (0.45), residues: 124 loop : -1.67 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.002 0.000 HIS C 149 PHE 0.043 0.001 PHE A 40 TYR 0.010 0.001 TYR A 26 ARG 0.008 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.417 Fit side-chains REVERT: A 82 LEU cc_start: 0.7427 (tt) cc_final: 0.6807 (mp) REVERT: A 119 GLN cc_start: 0.6320 (tm-30) cc_final: 0.5872 (tt0) REVERT: B 82 LEU cc_start: 0.7423 (tt) cc_final: 0.6774 (mp) REVERT: B 119 GLN cc_start: 0.6307 (tm-30) cc_final: 0.5876 (tt0) REVERT: C 82 LEU cc_start: 0.7426 (tt) cc_final: 0.6775 (mp) REVERT: C 119 GLN cc_start: 0.6316 (tm-30) cc_final: 0.5868 (tt0) REVERT: D 82 LEU cc_start: 0.7431 (tt) cc_final: 0.6778 (mp) REVERT: D 119 GLN cc_start: 0.6301 (tm-30) cc_final: 0.5868 (tt0) outliers start: 4 outliers final: 0 residues processed: 124 average time/residue: 0.2240 time to fit residues: 42.2482 Evaluate side-chains 110 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13492 Z= 0.158 Angle : 0.605 11.055 18156 Z= 0.278 Chirality : 0.043 0.241 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.922 163.123 2372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.90 % Allowed : 20.00 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1544 helix: 2.07 (0.18), residues: 896 sheet: -0.21 (0.45), residues: 124 loop : -1.62 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.001 0.000 HIS D 149 PHE 0.045 0.001 PHE A 40 TYR 0.008 0.001 TYR C 26 ARG 0.005 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.382 Fit side-chains REVERT: A 82 LEU cc_start: 0.7428 (tt) cc_final: 0.6798 (mp) REVERT: A 114 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8261 (tptt) REVERT: A 119 GLN cc_start: 0.6303 (tm-30) cc_final: 0.5844 (tt0) REVERT: B 82 LEU cc_start: 0.7432 (tt) cc_final: 0.6724 (mp) REVERT: B 114 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8184 (tptt) REVERT: B 119 GLN cc_start: 0.6268 (tm-30) cc_final: 0.5824 (tt0) REVERT: C 82 LEU cc_start: 0.7438 (tt) cc_final: 0.6732 (mp) REVERT: C 114 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8134 (tptt) REVERT: C 119 GLN cc_start: 0.6278 (tm-30) cc_final: 0.5834 (tt0) REVERT: D 82 LEU cc_start: 0.7440 (tt) cc_final: 0.6753 (mp) REVERT: D 119 GLN cc_start: 0.6258 (tm-30) cc_final: 0.5807 (tt0) outliers start: 12 outliers final: 2 residues processed: 129 average time/residue: 0.2324 time to fit residues: 45.0394 Evaluate side-chains 114 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain D residue 156 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 126 optimal weight: 0.3980 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.7996 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13492 Z= 0.163 Angle : 0.630 9.556 18156 Z= 0.283 Chirality : 0.043 0.210 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.810 163.410 2372 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.45 % Allowed : 20.90 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1544 helix: 2.08 (0.18), residues: 896 sheet: -0.18 (0.45), residues: 124 loop : -1.63 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.000 HIS A 99 PHE 0.046 0.001 PHE A 40 TYR 0.008 0.001 TYR A 26 ARG 0.007 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.565 Fit side-chains REVERT: A 82 LEU cc_start: 0.7438 (tt) cc_final: 0.6776 (mp) REVERT: A 114 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8459 (tptt) REVERT: A 119 GLN cc_start: 0.6337 (tm-30) cc_final: 0.5879 (tt0) REVERT: B 82 LEU cc_start: 0.7438 (tt) cc_final: 0.6724 (mp) REVERT: B 114 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8370 (tptt) REVERT: B 119 GLN cc_start: 0.6350 (tm-30) cc_final: 0.5901 (tt0) REVERT: B 234 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 82 LEU cc_start: 0.7450 (tt) cc_final: 0.6738 (mp) REVERT: C 114 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8287 (tptt) REVERT: C 119 GLN cc_start: 0.6333 (tm-30) cc_final: 0.5873 (tt0) REVERT: D 82 LEU cc_start: 0.7432 (tt) cc_final: 0.6749 (mp) REVERT: D 119 GLN cc_start: 0.6250 (tm-30) cc_final: 0.5824 (tt0) outliers start: 6 outliers final: 2 residues processed: 125 average time/residue: 0.2386 time to fit residues: 45.4602 Evaluate side-chains 120 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain D residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 123 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13492 Z= 0.177 Angle : 0.640 11.047 18156 Z= 0.289 Chirality : 0.043 0.249 2100 Planarity : 0.004 0.035 2172 Dihedral : 15.758 163.414 2372 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.67 % Allowed : 21.79 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1544 helix: 2.06 (0.18), residues: 896 sheet: -0.18 (0.46), residues: 124 loop : -1.58 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.000 HIS B 149 PHE 0.062 0.001 PHE A 40 TYR 0.006 0.001 TYR A 211 ARG 0.007 0.000 ARG A 111 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 82 LEU cc_start: 0.7460 (tt) cc_final: 0.6803 (mp) REVERT: A 113 LEU cc_start: 0.7972 (mp) cc_final: 0.7640 (pp) REVERT: A 119 GLN cc_start: 0.6269 (tm-30) cc_final: 0.5810 (tt0) REVERT: B 82 LEU cc_start: 0.7440 (tt) cc_final: 0.6755 (mp) REVERT: B 113 LEU cc_start: 0.7959 (mp) cc_final: 0.7623 (pp) REVERT: B 119 GLN cc_start: 0.6284 (tm-30) cc_final: 0.5820 (tt0) REVERT: C 82 LEU cc_start: 0.7466 (tt) cc_final: 0.6745 (mp) REVERT: C 113 LEU cc_start: 0.8049 (mp) cc_final: 0.7689 (pp) REVERT: C 114 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8246 (tptt) REVERT: C 119 GLN cc_start: 0.6267 (tm-30) cc_final: 0.5816 (tt0) REVERT: D 82 LEU cc_start: 0.7432 (tt) cc_final: 0.6755 (mp) REVERT: D 119 GLN cc_start: 0.6278 (tm-30) cc_final: 0.5798 (tt0) outliers start: 9 outliers final: 0 residues processed: 128 average time/residue: 0.2310 time to fit residues: 44.4676 Evaluate side-chains 121 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 0.0670 chunk 15 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120380 restraints weight = 21210.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123351 restraints weight = 13833.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125044 restraints weight = 10748.823| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13492 Z= 0.155 Angle : 0.623 8.767 18156 Z= 0.285 Chirality : 0.042 0.157 2100 Planarity : 0.004 0.036 2172 Dihedral : 15.661 163.167 2372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.07 % Allowed : 21.94 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1544 helix: 2.10 (0.18), residues: 896 sheet: -0.19 (0.46), residues: 124 loop : -1.55 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 176 HIS 0.001 0.000 HIS A 99 PHE 0.057 0.001 PHE A 40 TYR 0.006 0.001 TYR D 26 ARG 0.006 0.000 ARG D 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.18 seconds wall clock time: 40 minutes 36.63 seconds (2436.63 seconds total)