Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 06:34:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usw_26741/04_2023/7usw_26741_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 78 5.16 5 C 9572 2.51 5 N 2282 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 675": "OE1" <-> "OE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 158": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14322 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4897 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 589} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4897 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 589} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 328 Unusual residues: {' CA': 2, '3PE': 1, 'CLR': 1, 'D12': 6, 'NAG': 1, 'PEE': 1, 'R16': 1, 'ZFC': 14} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 360 Unusual residues: {' CA': 2, '3PE': 1, 'CLR': 1, 'D12': 6, 'NAG': 1, 'PEE': 1, 'R16': 3, 'ZFC': 14} Classifications: {'undetermined': 29} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {'PLM': 1, 'ZFC': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {'PLM': 1, 'ZFC': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.23, per 1000 atoms: 0.57 Number of scatterers: 14322 At special positions: 0 Unit cell: (133.401, 108.231, 108.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 78 16.00 P 4 15.00 O 2378 8.00 N 2282 7.00 C 9572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " 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=5, symmetry=0 Links applied NAG-ASN " NAG A1327 " - " ASN A 209 " " NAG B1329 " - " ASN B 209 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 2 sheets defined 68.0% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 100 through 120 removed outlier: 4.564A pdb=" N SER A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LYS A 120 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.993A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 167 through 190 removed outlier: 3.981A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.915A pdb=" N THR A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 4.133A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N HIS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 262 through 289 removed outlier: 3.607A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 319 through 342 removed outlier: 3.585A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 380 removed outlier: 3.591A pdb=" N CYS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 416 removed outlier: 4.337A pdb=" N VAL A 395 " --> pdb=" O LYS A 392 " (cutoff:3.500A) Proline residue: A 396 - end of helix removed outlier: 4.082A pdb=" N VAL A 399 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 400 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A 406 " --> pdb=" O THR A 403 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 421 through 458 Processing helix chain 'A' and resid 668 through 694 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 725 through 743 Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.801A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 833 removed outlier: 4.325A pdb=" N ARG A 831 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 849 removed outlier: 3.828A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 885 Proline residue: A 856 - end of helix Processing helix chain 'B' and resid 76 through 92 Processing helix chain 'B' and resid 100 through 120 removed outlier: 4.560A pdb=" N SER B 119 " --> pdb=" O GLU B 115 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 149 removed outlier: 4.006A pdb=" N TYR B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.988A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.895A pdb=" N THR B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.148A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N HIS B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 262 through 289 removed outlier: 3.604A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.556A pdb=" N LYS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 380 removed outlier: 3.581A pdb=" N CYS B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.347A pdb=" N VAL B 395 " --> pdb=" O LYS B 392 " (cutoff:3.500A) Proline residue: B 396 - end of helix removed outlier: 4.074A pdb=" N VAL B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER B 400 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) Proline residue: B 407 - end of helix Processing helix chain 'B' and resid 421 through 458 Processing helix chain 'B' and resid 668 through 694 Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 725 through 743 Processing helix chain 'B' and resid 749 through 770 removed outlier: 3.802A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 833 removed outlier: 4.341A pdb=" N ARG B 831 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 849 removed outlier: 3.870A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 849 " --> pdb=" O ILE B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 885 Proline residue: B 856 - end of helix Processing helix chain 'C' and resid 22 through 31 Processing helix chain 'C' and resid 36 through 49 Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 118 through 129 Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 180 through 187 Processing helix chain 'C' and resid 193 through 196 No H-bonds generated for 'chain 'C' and resid 193 through 196' Processing helix chain 'D' and resid 24 through 44 Processing helix chain 'D' and resid 54 through 62 Processing helix chain 'E' and resid 22 through 31 Processing helix chain 'E' and resid 36 through 49 Processing helix chain 'E' and resid 62 through 65 No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 77 through 80 No H-bonds generated for 'chain 'E' and resid 77 through 80' Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 180 through 187 Processing helix chain 'E' and resid 193 through 196 No H-bonds generated for 'chain 'E' and resid 193 through 196' Processing helix chain 'F' and resid 24 through 44 Processing helix chain 'F' and resid 54 through 62 Processing sheet with id= A, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= B, first strand: chain 'E' and resid 67 through 69 788 hydrogen bonds defined for protein. 2268 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: 4.05 Time building geometry restraints manager: 6.43 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: 2100 1.31 - 1.43: 3931 1.43 - 1.56: 8415 1.56 - 1.69: 8 1.69 - 1.81: 130 Bond restraints: 14584 Sorted by residual: bond pdb=" C21 3PE B1305 " pdb=" O21 3PE B1305 " ideal model delta sigma weight residual 1.316 1.397 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C21 3PE A1304 " pdb=" O21 3PE A1304 " ideal model delta sigma weight residual 1.316 1.397 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C30 PEE B1304 " pdb=" O3 PEE B1304 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C10 PEE B1304 " pdb=" O2 PEE B1304 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14579 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.07: 334 107.07 - 113.80: 8388 113.80 - 120.53: 5731 120.53 - 127.27: 4920 127.27 - 134.00: 137 Bond angle restraints: 19510 Sorted by residual: angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 109.24 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" O3P PEE B1304 " pdb=" P PEE B1304 " pdb=" O4P PEE B1304 " ideal model delta sigma weight residual 92.91 109.20 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" O12 3PE A1304 " pdb=" P 3PE A1304 " pdb=" O14 3PE A1304 " ideal model delta sigma weight residual 123.79 109.30 14.49 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O12 3PE B1305 " pdb=" P 3PE B1305 " pdb=" O14 3PE B1305 " ideal model delta sigma weight residual 123.79 109.32 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O1P PEE A1303 " pdb=" P PEE A1303 " pdb=" O2P PEE A1303 " ideal model delta sigma weight residual 119.43 109.35 10.08 3.00e+00 1.11e-01 1.13e+01 ... (remaining 19505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 7802 21.38 - 42.76: 823 42.76 - 64.14: 95 64.14 - 85.52: 9 85.52 - 106.90: 5 Dihedral angle restraints: 8734 sinusoidal: 3788 harmonic: 4946 Sorted by residual: dihedral pdb=" N PEE B1304 " pdb=" C4 PEE B1304 " pdb=" C5 PEE B1304 " pdb=" O4P PEE B1304 " ideal model delta sinusoidal sigma weight residual -56.97 -163.87 106.90 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" N PEE A1303 " pdb=" C4 PEE A1303 " pdb=" C5 PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sinusoidal sigma weight residual -56.97 -163.82 106.85 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" CA MET D 46 " pdb=" C MET D 46 " pdb=" N ARG D 47 " pdb=" CA ARG D 47 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2026 0.074 - 0.148: 134 0.148 - 0.222: 4 0.222 - 0.296: 1 0.296 - 0.371: 1 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG B1329 " pdb=" ND2 ASN B 209 " pdb=" C2 NAG B1329 " pdb=" O5 NAG B1329 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG A1327 " pdb=" ND2 ASN A 209 " pdb=" C2 NAG A1327 " pdb=" O5 NAG A1327 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2 PEE B1304 " pdb=" C1 PEE B1304 " pdb=" C3 PEE B1304 " pdb=" O2 PEE B1304 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2163 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1329 " -0.276 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" C7 NAG B1329 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1329 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1329 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG B1329 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1327 " 0.275 2.00e-02 2.50e+03 2.35e-01 6.92e+02 pdb=" C7 NAG A1327 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1327 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG A1327 " -0.395 2.00e-02 2.50e+03 pdb=" O7 NAG A1327 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.096 2.00e-02 2.50e+03 1.21e-01 1.83e+02 pdb=" CG ASN A 209 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG A1327 " 0.143 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3188 2.78 - 3.31: 13206 3.31 - 3.84: 23522 3.84 - 4.37: 26222 4.37 - 4.90: 47465 Nonbonded interactions: 113603 Sorted by model distance: nonbonded pdb=" O TYR C 28 " pdb=" OG1 THR C 32 " model vdw 2.254 2.440 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.277 2.440 nonbonded pdb=" SG CYS F 44 " pdb=" C1 PLM F 204 " model vdw 2.286 3.630 nonbonded pdb=" OE2 GLU B 196 " pdb=" NZ LYS B 215 " model vdw 2.286 2.520 nonbonded pdb=" OE2 GLU A 196 " pdb=" NZ LYS A 215 " model vdw 2.288 2.520 ... (remaining 113598 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 75 through 886 or resid 1302 or resid 1306 or resid 1308 t \ hrough 1309 or resid 1316 through 1319 or (resid 1320 through 1321 and (name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or resid 13 \ 22 through 1323 or resid 1325)) selection = (chain 'B' and (resid 75 through 886 or resid 1302 or resid 1306 or resid 1308 t \ hrough 1309 or (resid 1316 and (name C1 or name C2 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 )) or resid 1317 or (resid 1318 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 ) \ ) or (resid 1319 and (name C1 or name C2 or name C3 or name C4 or name C5 or nam \ e C6 or name C7 or name C8 )) or (resid 1320 through 1321 and (name C1 or name C \ 2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 1322 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 )) or resid 1323 or resid 1325)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 14.260 Check model and map are aligned: 0.270 Set scattering table: 0.130 Process input model: 37.640 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.110 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.004 0.081 14584 Z= 0.239 Angle : 0.778 16.332 19510 Z= 0.339 Chirality : 0.040 0.371 2166 Planarity : 0.008 0.235 2342 Dihedral : 15.906 106.901 5516 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.21), residues: 1660 helix: 2.54 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 174 average time/residue: 0.3303 time to fit residues: 80.1827 Evaluate side-chains 170 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1219 time to fit residues: 2.6680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 95 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 14584 Z= 0.160 Angle : 0.452 7.315 19510 Z= 0.234 Chirality : 0.038 0.121 2166 Planarity : 0.004 0.054 2342 Dihedral : 7.960 68.732 2326 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.10 % 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: 2.24 (0.21), residues: 1660 helix: 2.55 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 494 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 183 average time/residue: 0.3103 time to fit residues: 79.7913 Evaluate side-chains 177 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1271 time to fit residues: 3.9222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 chunk 101 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14584 Z= 0.174 Angle : 0.460 7.126 19510 Z= 0.237 Chirality : 0.038 0.122 2166 Planarity : 0.004 0.054 2342 Dihedral : 7.750 59.164 2326 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.21), residues: 1660 helix: 2.60 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.793 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 187 average time/residue: 0.3304 time to fit residues: 85.9516 Evaluate side-chains 181 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1278 time to fit residues: 5.1763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14584 Z= 0.164 Angle : 0.456 7.287 19510 Z= 0.235 Chirality : 0.038 0.123 2166 Planarity : 0.004 0.054 2342 Dihedral : 7.675 65.522 2326 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.21), residues: 1660 helix: 2.60 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.572 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 183 average time/residue: 0.3322 time to fit residues: 84.9690 Evaluate side-chains 175 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1383 time to fit residues: 3.8824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 135 optimal weight: 0.0070 chunk 109 optimal weight: 0.0970 chunk 0 optimal weight: 40.0000 chunk 80 optimal weight: 0.9980 chunk 142 optimal weight: 0.0030 chunk 40 optimal weight: 0.7980 overall best weight: 0.3206 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 14584 Z= 0.126 Angle : 0.435 7.284 19510 Z= 0.226 Chirality : 0.037 0.123 2166 Planarity : 0.003 0.053 2342 Dihedral : 7.362 66.399 2326 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.21), residues: 1660 helix: 2.71 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.538 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 176 average time/residue: 0.3161 time to fit residues: 78.6315 Evaluate side-chains 170 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1259 time to fit residues: 2.9502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 158 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 14584 Z= 0.148 Angle : 0.447 7.351 19510 Z= 0.231 Chirality : 0.038 0.121 2166 Planarity : 0.003 0.055 2342 Dihedral : 7.351 68.040 2326 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.21), residues: 1660 helix: 2.68 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 502 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.662 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 183 average time/residue: 0.3005 time to fit residues: 77.9716 Evaluate side-chains 177 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 1.392 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1197 time to fit residues: 3.5377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14584 Z= 0.202 Angle : 0.487 7.566 19510 Z= 0.251 Chirality : 0.039 0.132 2166 Planarity : 0.004 0.057 2342 Dihedral : 7.794 75.216 2326 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1660 helix: 2.58 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.832 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 179 average time/residue: 0.3294 time to fit residues: 83.7565 Evaluate side-chains 175 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.626 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1306 time to fit residues: 3.0744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 0.0050 chunk 30 optimal weight: 0.0470 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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: 0.7698 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 14584 Z= 0.144 Angle : 0.462 8.729 19510 Z= 0.238 Chirality : 0.038 0.134 2166 Planarity : 0.003 0.054 2342 Dihedral : 7.511 77.636 2326 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.21), residues: 1660 helix: 2.65 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.595 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 0.3243 time to fit residues: 77.2014 Evaluate side-chains 168 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1275 time to fit residues: 2.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 20.0000 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 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: 0.7724 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 14584 Z= 0.191 Angle : 0.487 8.643 19510 Z= 0.251 Chirality : 0.039 0.135 2166 Planarity : 0.004 0.056 2342 Dihedral : 7.726 81.645 2326 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1660 helix: 2.59 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.737 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.3207 time to fit residues: 76.9198 Evaluate side-chains 165 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.672 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 14584 Z= 0.151 Angle : 0.468 8.217 19510 Z= 0.245 Chirality : 0.038 0.129 2166 Planarity : 0.003 0.055 2342 Dihedral : 7.560 84.732 2326 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.21), residues: 1660 helix: 2.59 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.571 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 167 average time/residue: 0.3361 time to fit residues: 78.8021 Evaluate side-chains 163 residues out of total 1506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.0060 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.207341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.160996 restraints weight = 14888.728| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 3.00 r_work: 0.3630 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 14584 Z= 0.139 Angle : 0.466 9.642 19510 Z= 0.242 Chirality : 0.038 0.158 2166 Planarity : 0.003 0.054 2342 Dihedral : 7.355 87.443 2326 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.21), residues: 1660 helix: 2.58 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 492 =============================================================================== Job complete usr+sys time: 2841.27 seconds wall clock time: 52 minutes 36.20 seconds (3156.20 seconds total)