Starting phenix.real_space_refine on Sat Dec 9 16:13:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/12_2023/8go8_34173_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 74 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 38 5.16 5 C 7280 2.51 5 N 1938 2.21 5 O 2239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 2": "OD1" <-> "OD2" Residue "M ASP 18": "OD1" <-> "OD2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11505 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2803 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2808 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1363 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 6.34, per 1000 atoms: 0.55 Number of scatterers: 11505 At special positions: 0 Unit cell: (112.238, 201.413, 99.9375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 10 15.00 O 2239 8.00 N 1938 7.00 C 7280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 2.2 seconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 30 sheets defined 4.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.849A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.850A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.489A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 288 through 290 removed outlier: 4.825A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 87 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 55 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 57 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N CYS A 59 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A 81 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 146 through 149 Processing sheet with id= E, first strand: chain 'A' and resid 183 through 189 Processing sheet with id= F, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.126A pdb=" N THR A 350 " --> pdb=" O TYR A 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 343 through 349 removed outlier: 3.560A pdb=" N PHE A 349 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 316 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= I, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.489A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 288 through 290 removed outlier: 4.825A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 87 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 55 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 57 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N CYS B 59 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 81 " --> pdb=" O CYS B 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 149 Processing sheet with id= L, first strand: chain 'B' and resid 183 through 189 Processing sheet with id= M, first strand: chain 'B' and resid 207 through 209 removed outlier: 6.127A pdb=" N THR B 350 " --> pdb=" O TYR B 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 343 through 349 removed outlier: 3.560A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 316 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.580A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 161 through 164 Processing sheet with id= S, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL I 8 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 117 through 119 removed outlier: 3.580A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 161 through 164 Processing sheet with id= W, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= X, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.799A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.535A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.636A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 177 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AB, first strand: chain 'M' and resid 11 through 13 removed outlier: 5.798A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.534A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.635A pdb=" N SER M 115 " --> pdb=" O ASN M 138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER M 177 " --> pdb=" O SER M 163 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 960 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: 3.70 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3708 1.34 - 1.46: 2688 1.46 - 1.58: 5291 1.58 - 1.69: 34 1.69 - 1.81: 48 Bond restraints: 11769 Sorted by residual: bond pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 11764 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 442 107.09 - 113.82: 6638 113.82 - 120.55: 4125 120.55 - 127.28: 4719 127.28 - 134.01: 133 Bond angle restraints: 16057 Sorted by residual: angle pdb=" CB TPO V 339 " pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 119.31 106.91 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB TPO U 339 " pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 119.31 106.94 12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CB TPO U 342 " pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO V 336 " pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO U 336 " pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 119.31 107.12 12.19 3.00e+00 1.11e-01 1.65e+01 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 6481 16.85 - 33.70: 458 33.70 - 50.54: 104 50.54 - 67.39: 14 67.39 - 84.24: 12 Dihedral angle restraints: 7069 sinusoidal: 2631 harmonic: 4438 Sorted by residual: dihedral pdb=" CB LYS A 226 " pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " pdb=" CE LYS A 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.52 -56.52 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CB LYS B 226 " pdb=" CG LYS B 226 " pdb=" CD LYS B 226 " pdb=" CE LYS B 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.45 -56.45 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG ARG B 65 " pdb=" CD ARG B 65 " pdb=" NE ARG B 65 " pdb=" CZ ARG B 65 " ideal model delta sinusoidal sigma weight residual 180.00 139.48 40.52 2 1.50e+01 4.44e-03 9.00e+00 ... (remaining 7066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1026 0.026 - 0.052: 516 0.052 - 0.079: 102 0.079 - 0.105: 119 0.105 - 0.131: 73 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA VAL L 95 " pdb=" N VAL L 95 " pdb=" C VAL L 95 " pdb=" CB VAL L 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA PHE U 335 " pdb=" N PHE U 335 " pdb=" C PHE U 335 " pdb=" CB PHE U 335 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 233 " pdb=" N ILE B 233 " pdb=" C ILE B 233 " pdb=" CB ILE B 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1833 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 159 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 358 " 0.006 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU B 358 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU B 358 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 359 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 158 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO I 159 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2153 2.78 - 3.31: 9830 3.31 - 3.84: 17832 3.84 - 4.37: 20140 4.37 - 4.90: 37099 Nonbonded interactions: 87054 Sorted by model distance: nonbonded pdb=" NE2 GLN L 125 " pdb=" O THR L 130 " model vdw 2.253 2.520 nonbonded pdb=" NE2 GLN M 125 " pdb=" O THR M 130 " model vdw 2.254 2.520 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.278 2.440 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.278 2.440 nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.290 2.440 ... (remaining 87049 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 7 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 368)) selection = (chain 'B' and (resid 7 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 190)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.980 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 0.109 11769 Z= 0.299 Angle : 0.607 12.405 16057 Z= 0.270 Chirality : 0.042 0.131 1836 Planarity : 0.003 0.034 2058 Dihedral : 12.950 84.237 4191 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 1.03 (0.23), residues: 1478 helix: 0.56 (0.84), residues: 34 sheet: 1.29 (0.21), residues: 644 loop : 0.25 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.002 0.000 HIS B 353 PHE 0.008 0.001 PHE V 335 TYR 0.008 0.001 TYR M 50 ARG 0.005 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2776 time to fit residues: 74.8922 Evaluate side-chains 121 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 134 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 248 GLN I 6 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11769 Z= 0.190 Angle : 0.539 12.252 16057 Z= 0.271 Chirality : 0.044 0.136 1836 Planarity : 0.004 0.038 2058 Dihedral : 4.184 37.874 1658 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.15 % Allowed : 7.96 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.22), residues: 1478 helix: -0.36 (0.68), residues: 46 sheet: 1.09 (0.20), residues: 706 loop : 0.33 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 164 HIS 0.003 0.001 HIS I 174 PHE 0.015 0.002 PHE M 117 TYR 0.027 0.001 TYR H 155 ARG 0.004 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.358 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 0.2720 time to fit residues: 51.4777 Evaluate side-chains 116 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1565 time to fit residues: 3.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11769 Z= 0.326 Angle : 0.575 13.192 16057 Z= 0.291 Chirality : 0.046 0.169 1836 Planarity : 0.004 0.033 2058 Dihedral : 4.396 36.005 1658 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.41 % Allowed : 9.76 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1478 helix: -0.74 (0.65), residues: 46 sheet: 1.01 (0.20), residues: 676 loop : 0.13 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 164 HIS 0.004 0.001 HIS B 362 PHE 0.016 0.002 PHE B 277 TYR 0.026 0.002 TYR A 249 ARG 0.004 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.264 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.2792 time to fit residues: 47.7298 Evaluate side-chains 108 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1030 time to fit residues: 2.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11769 Z= 0.276 Angle : 0.548 12.052 16057 Z= 0.274 Chirality : 0.044 0.151 1836 Planarity : 0.004 0.034 2058 Dihedral : 4.388 36.535 1658 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.23 % Allowed : 11.73 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1478 helix: -0.67 (0.68), residues: 46 sheet: 0.92 (0.20), residues: 676 loop : 0.08 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 50 HIS 0.004 0.001 HIS A 210 PHE 0.014 0.002 PHE A 277 TYR 0.021 0.002 TYR I 155 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.374 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.2824 time to fit residues: 46.3687 Evaluate side-chains 109 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1085 time to fit residues: 3.1811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 98 optimal weight: 0.0010 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11769 Z= 0.252 Angle : 0.529 11.403 16057 Z= 0.265 Chirality : 0.044 0.219 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.345 37.340 1658 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.49 % Allowed : 12.96 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1478 helix: -0.60 (0.69), residues: 46 sheet: 0.87 (0.20), residues: 676 loop : 0.05 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 164 HIS 0.003 0.001 HIS B 362 PHE 0.013 0.001 PHE A 277 TYR 0.015 0.001 TYR I 155 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.2818 time to fit residues: 44.2902 Evaluate side-chains 107 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1241 time to fit residues: 2.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 0.0970 chunk 66 optimal weight: 0.0020 chunk 11 optimal weight: 0.0670 chunk 47 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 overall best weight: 0.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11769 Z= 0.129 Angle : 0.484 9.381 16057 Z= 0.239 Chirality : 0.043 0.151 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.071 36.693 1658 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.57 % Allowed : 13.54 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1478 helix: -0.61 (0.70), residues: 46 sheet: 1.03 (0.20), residues: 682 loop : 0.17 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 164 HIS 0.001 0.000 HIS B 159 PHE 0.011 0.001 PHE M 117 TYR 0.015 0.001 TYR I 155 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 128 average time/residue: 0.2787 time to fit residues: 50.7143 Evaluate side-chains 118 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1073 time to fit residues: 2.2157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11769 Z= 0.238 Angle : 0.519 10.621 16057 Z= 0.259 Chirality : 0.043 0.137 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.138 37.611 1658 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.74 % Allowed : 14.52 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1478 helix: -0.56 (0.70), residues: 46 sheet: 1.08 (0.20), residues: 676 loop : 0.15 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 164 HIS 0.003 0.001 HIS B 362 PHE 0.013 0.001 PHE B 277 TYR 0.023 0.001 TYR I 155 ARG 0.006 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 111 average time/residue: 0.2652 time to fit residues: 41.7368 Evaluate side-chains 114 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1271 time to fit residues: 2.8685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.0570 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11769 Z= 0.271 Angle : 0.540 10.888 16057 Z= 0.271 Chirality : 0.044 0.146 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.263 37.912 1658 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.41 % Allowed : 14.85 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1478 helix: -0.63 (0.71), residues: 46 sheet: 0.95 (0.20), residues: 678 loop : 0.09 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 164 HIS 0.003 0.001 HIS B 362 PHE 0.012 0.001 PHE A 277 TYR 0.023 0.002 TYR I 155 ARG 0.006 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 110 average time/residue: 0.2776 time to fit residues: 43.0663 Evaluate side-chains 104 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1017 time to fit residues: 2.1141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11769 Z= 0.243 Angle : 0.534 10.537 16057 Z= 0.266 Chirality : 0.044 0.147 1836 Planarity : 0.004 0.047 2058 Dihedral : 4.225 37.799 1658 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.66 % Allowed : 14.93 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1478 helix: -0.61 (0.71), residues: 46 sheet: 0.89 (0.20), residues: 686 loop : 0.14 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 164 HIS 0.003 0.001 HIS B 362 PHE 0.011 0.001 PHE A 277 TYR 0.022 0.001 TYR H 155 ARG 0.014 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.2989 time to fit residues: 44.4549 Evaluate side-chains 106 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1370 time to fit residues: 2.9702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11769 Z= 0.206 Angle : 0.524 10.495 16057 Z= 0.260 Chirality : 0.043 0.149 1836 Planarity : 0.004 0.057 2058 Dihedral : 4.155 37.696 1658 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.33 % Allowed : 15.18 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1478 helix: -0.57 (0.72), residues: 46 sheet: 0.94 (0.20), residues: 684 loop : 0.16 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 164 HIS 0.002 0.000 HIS B 362 PHE 0.011 0.001 PHE B 277 TYR 0.023 0.001 TYR I 155 ARG 0.015 0.001 ARG B 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.412 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 110 average time/residue: 0.2636 time to fit residues: 41.3724 Evaluate side-chains 106 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1042 time to fit residues: 2.1859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.4980 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112238 restraints weight = 16389.278| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.30 r_work: 0.3168 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11769 Z= 0.232 Angle : 0.529 10.499 16057 Z= 0.264 Chirality : 0.044 0.155 1836 Planarity : 0.004 0.060 2058 Dihedral : 4.170 37.892 1658 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.25 % Allowed : 14.85 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1478 helix: -0.46 (0.72), residues: 46 sheet: 0.87 (0.20), residues: 686 loop : 0.15 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 164 HIS 0.003 0.001 HIS B 362 PHE 0.011 0.001 PHE L 117 TYR 0.025 0.001 TYR H 155 ARG 0.015 0.001 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.59 seconds wall clock time: 45 minutes 21.74 seconds (2721.74 seconds total)