Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 05:15:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usx_26742/04_2023/7usx_26742_updated.pdb" } resolution = 3.09 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 9466 2.51 5 N 2282 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 727": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 169": "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: 14220 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4883 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 18, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 54 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: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 353 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 264 Unusual residues: {' CA': 2, 'CLR': 1, 'D12': 12, 'NAG': 1, 'PEE': 1, 'R16': 4} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 39 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'3PE': 1, 'D12': 2, 'PLM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 8.15, per 1000 atoms: 0.57 Number of scatterers: 14220 At special positions: 0 Unit cell: (133.401, 103.197, 106.553, 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 2382 8.00 N 2282 7.00 C 9466 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=2, symmetry=0 Links applied NAG-ASN " NAG A1321 " - " ASN A 209 " " NAG B1321 " - " ASN B 209 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.82 Conformation dependent library (CDL) restraints added in 2.1 seconds 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 2 sheets defined 66.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 123 through 149 removed outlier: 3.989A pdb=" N TYR A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.258A 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: 4.055A 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 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 219 through 225 removed outlier: 4.463A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N HIS A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 225' 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 290 removed outlier: 3.574A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 Processing helix chain 'A' and resid 319 through 342 removed outlier: 3.647A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 380 Processing helix chain 'A' and resid 395 through 417 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 741 Processing helix chain 'A' and resid 749 through 771 removed outlier: 3.827A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 833 removed outlier: 4.309A pdb=" N ARG A 831 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.950A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 882 Proline residue: A 856 - end of helix removed outlier: 3.539A pdb=" N SER A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 880 " --> pdb=" O ARG A 876 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 100 through 117 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: 4.253A 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: 4.044A 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 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 219 through 225 removed outlier: 4.468A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N HIS B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 225' 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 290 removed outlier: 3.576A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.671A pdb=" N LYS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 380 Processing helix chain 'B' and resid 395 through 417 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 741 Processing helix chain 'B' and resid 749 through 771 removed outlier: 3.826A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 833 removed outlier: 4.299A pdb=" N ARG B 831 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 847 removed outlier: 3.950A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 882 Proline residue: B 856 - end of helix removed outlier: 3.537A pdb=" N SER B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR B 880 " --> pdb=" O ARG B 876 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) 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 91 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 150 Processing helix chain 'C' and resid 156 through 170 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 91 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 150 Processing helix chain 'E' and resid 156 through 170 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 69 778 hydrogen bonds defined for protein. 2310 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: 3.91 Time building geometry restraints manager: 6.23 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: 3916 1.43 - 1.56: 8342 1.56 - 1.68: 8 1.68 - 1.81: 130 Bond restraints: 14496 Sorted by residual: bond pdb=" C21 3PE F 201 " pdb=" O21 3PE F 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C21 3PE D 201 " pdb=" O21 3PE D 201 " ideal model delta sigma weight residual 1.316 1.398 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C30 PEE B1303 " pdb=" O3 PEE B1303 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+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 1.24e+01 bond pdb=" C10 PEE B1303 " pdb=" O2 PEE B1303 " ideal model delta sigma weight residual 1.332 1.400 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.80: 244 105.80 - 112.85: 7946 112.85 - 119.91: 4732 119.91 - 126.96: 6347 126.96 - 134.01: 159 Bond angle restraints: 19428 Sorted by residual: angle pdb=" O3P PEE B1303 " pdb=" P PEE B1303 " pdb=" O4P PEE B1303 " ideal model delta sigma weight residual 92.91 108.85 -15.94 3.00e+00 1.11e-01 2.82e+01 angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 108.82 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O12 3PE D 201 " pdb=" P 3PE D 201 " pdb=" O14 3PE D 201 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE F 201 " pdb=" P 3PE F 201 " pdb=" O14 3PE F 201 " ideal model delta sigma weight residual 123.79 109.46 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" C ARG B 334 " pdb=" N GLU B 335 " pdb=" CA GLU B 335 " ideal model delta sigma weight residual 120.72 114.36 6.36 1.67e+00 3.59e-01 1.45e+01 ... (remaining 19423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 7760 21.22 - 42.45: 765 42.45 - 63.67: 141 63.67 - 84.90: 9 84.90 - 106.12: 7 Dihedral angle restraints: 8682 sinusoidal: 3754 harmonic: 4928 Sorted by residual: dihedral pdb=" CB CYS B 667 " pdb=" SG CYS B 667 " pdb=" SG CYS B 816 " pdb=" CB CYS B 816 " ideal model delta sinusoidal sigma weight residual -86.00 -142.54 56.54 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS A 667 " pdb=" SG CYS A 667 " pdb=" SG CYS A 816 " pdb=" CB CYS A 816 " ideal model delta sinusoidal sigma weight residual -86.00 -140.14 54.14 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C10 CLR A1308 " pdb=" C1 CLR A1308 " pdb=" C2 CLR A1308 " pdb=" C3 CLR A1308 " ideal model delta sinusoidal sigma weight residual -56.83 49.29 -106.12 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 8679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1566 0.041 - 0.081: 503 0.081 - 0.122: 79 0.122 - 0.162: 2 0.162 - 0.203: 10 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA GLU B 335 " pdb=" N GLU B 335 " pdb=" C GLU B 335 " pdb=" CB GLU B 335 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU A 335 " pdb=" N GLU A 335 " pdb=" C GLU A 335 " pdb=" CB GLU A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" C2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C3 PEE A1303 " pdb=" O2 PEE A1303 " both_signs ideal model delta sigma weight residual False -2.33 -2.50 0.17 2.00e-01 2.50e+01 7.41e-01 ... (remaining 2157 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG B1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B1321 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG B1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1321 " 0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG A1321 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1321 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG A1321 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1321 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.155 2.00e-02 2.50e+03 2.83e-01 9.98e+02 pdb=" CG ASN A 209 " -0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.104 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.501 2.00e-02 2.50e+03 pdb=" C1 NAG A1321 " 0.326 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2314 2.76 - 3.29: 13308 3.29 - 3.83: 23368 3.83 - 4.36: 26182 4.36 - 4.90: 47244 Nonbonded interactions: 112416 Sorted by model distance: nonbonded pdb=" O PRO E 63 " pdb=" OG SER E 101 " model vdw 2.223 2.440 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.248 2.440 nonbonded pdb=" NH2 ARG A 94 " pdb=" O GLN C 29 " model vdw 2.250 2.520 nonbonded pdb=" OD2 ASP B 683 " pdb=" NZ LYS B 756 " model vdw 2.253 2.520 nonbonded pdb=" NH2 ARG B 94 " pdb=" O GLN E 29 " model vdw 2.253 2.520 ... (remaining 112411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.380 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: 14.110 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 37.190 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 0.082 14496 Z= 0.245 Angle : 0.863 15.940 19428 Z= 0.370 Chirality : 0.040 0.203 2160 Planarity : 0.009 0.296 2340 Dihedral : 16.308 106.121 5476 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 1.65 (0.21), residues: 1654 helix: 2.28 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.381 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.2582 time to fit residues: 62.9937 Evaluate side-chains 159 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.527 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1223 time to fit residues: 2.6108 ------------------------------------------------------------------------------- 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: 0.6980 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 144 ASN B 439 ASN B 731 HIS C 99 ASN E 99 ASN E 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14496 Z= 0.225 Angle : 0.521 9.062 19428 Z= 0.263 Chirality : 0.040 0.164 2160 Planarity : 0.004 0.066 2340 Dihedral : 8.991 106.389 2270 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.34 % 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: 1.63 (0.21), residues: 1654 helix: 2.27 (0.15), residues: 1132 sheet: None (None), residues: 0 loop : -1.75 (0.25), residues: 522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 182 average time/residue: 0.2361 time to fit residues: 65.3919 Evaluate side-chains 174 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.669 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1390 time to fit residues: 6.4752 ------------------------------------------------------------------------------- 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: 9.9990 chunk 46 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 149 optimal weight: 0.0370 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS E 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 14496 Z= 0.130 Angle : 0.455 6.960 19428 Z= 0.233 Chirality : 0.037 0.181 2160 Planarity : 0.004 0.062 2340 Dihedral : 8.298 105.406 2270 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 1.58 % 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: 1.95 (0.21), residues: 1654 helix: 2.52 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.66 (0.25), residues: 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 178 average time/residue: 0.2419 time to fit residues: 65.8759 Evaluate side-chains 159 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1303 time to fit residues: 3.8735 ------------------------------------------------------------------------------- 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: 2.9990 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.0040 chunk 42 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 HIS B 144 ASN B 731 HIS C 99 ASN E 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14496 Z= 0.211 Angle : 0.497 7.646 19428 Z= 0.253 Chirality : 0.039 0.194 2160 Planarity : 0.004 0.066 2340 Dihedral : 8.297 106.324 2270 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 2.82 % 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: 1.81 (0.21), residues: 1654 helix: 2.40 (0.15), residues: 1134 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 520 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 184 average time/residue: 0.2417 time to fit residues: 68.2739 Evaluate side-chains 176 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1364 time to fit residues: 7.5722 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 80 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 731 HIS B 144 ASN B 394 GLN B 731 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14496 Z= 0.174 Angle : 0.474 7.329 19428 Z= 0.242 Chirality : 0.038 0.149 2160 Planarity : 0.004 0.064 2340 Dihedral : 8.043 106.179 2270 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1654 helix: 2.42 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -1.72 (0.25), residues: 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 175 average time/residue: 0.2481 time to fit residues: 66.6569 Evaluate side-chains 161 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1351 time to fit residues: 4.1833 ------------------------------------------------------------------------------- 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: 0.0670 chunk 142 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 731 HIS C 99 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14496 Z= 0.181 Angle : 0.486 6.819 19428 Z= 0.250 Chirality : 0.039 0.211 2160 Planarity : 0.004 0.064 2340 Dihedral : 7.950 106.211 2270 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 1.79 % 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: 1.81 (0.21), residues: 1654 helix: 2.40 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 173 average time/residue: 0.2528 time to fit residues: 66.7300 Evaluate side-chains 166 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1364 time to fit residues: 5.9047 ------------------------------------------------------------------------------- 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: 0.7980 chunk 115 optimal weight: 0.1980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN A 731 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 HIS ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14496 Z= 0.152 Angle : 0.477 6.916 19428 Z= 0.245 Chirality : 0.038 0.219 2160 Planarity : 0.004 0.063 2340 Dihedral : 7.704 105.971 2270 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 1.90 (0.21), residues: 1654 helix: 2.48 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 170 average time/residue: 0.2389 time to fit residues: 62.0756 Evaluate side-chains 161 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1322 time to fit residues: 3.5411 ------------------------------------------------------------------------------- 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: 0.6980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14496 Z= 0.201 Angle : 0.500 7.013 19428 Z= 0.257 Chirality : 0.039 0.163 2160 Planarity : 0.004 0.065 2340 Dihedral : 7.801 106.572 2270 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 1.24 % 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: 1.77 (0.21), residues: 1654 helix: 2.35 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 165 average time/residue: 0.2543 time to fit residues: 64.4413 Evaluate side-chains 166 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1393 time to fit residues: 5.0703 ------------------------------------------------------------------------------- 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: 1.9990 chunk 151 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS B 144 ASN ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 14496 Z= 0.179 Angle : 0.499 11.827 19428 Z= 0.255 Chirality : 0.039 0.236 2160 Planarity : 0.004 0.064 2340 Dihedral : 7.726 106.332 2270 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.41 % 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: 1.79 (0.21), residues: 1654 helix: 2.36 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.67 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 160 average time/residue: 0.2617 time to fit residues: 63.5477 Evaluate side-chains 160 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1354 time to fit residues: 3.3838 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 150 optimal weight: 0.0570 chunk 130 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 14496 Z= 0.145 Angle : 0.481 9.211 19428 Z= 0.246 Chirality : 0.037 0.181 2160 Planarity : 0.004 0.062 2340 Dihedral : 7.502 105.860 2270 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1654 helix: 2.47 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3308 Ramachandran restraints generated. 1654 Oldfield, 0 Emsley, 1654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 164 average time/residue: 0.2656 time to fit residues: 66.4010 Evaluate side-chains 161 residues out of total 1502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1338 time to fit residues: 3.4749 ------------------------------------------------------------------------------- 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: 2.9990 chunk 138 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 0.0570 chunk 54 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.209160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.149109 restraints weight = 14283.165| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.07 r_work: 0.3483 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 14496 Z= 0.175 Angle : 0.505 14.745 19428 Z= 0.256 Chirality : 0.038 0.186 2160 Planarity : 0.004 0.063 2340 Dihedral : 7.525 106.367 2270 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: 1.86 (0.21), residues: 1654 helix: 2.41 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 510 =============================================================================== Job complete usr+sys time: 2980.73 seconds wall clock time: 54 minutes 52.72 seconds (3292.72 seconds total)