Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 00:01:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7w_21573/04_2023/6w7w_21573.pdb" } resolution = 3.9 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= 0.999 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 871 5.49 5 S 33 5.16 5 C 13446 2.51 5 N 5026 2.21 5 O 7507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 15": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "E PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "N ASP 17": "OD1" <-> "OD2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "O PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P GLU 60": "OE1" <-> "OE2" Residue "P ARG 65": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "S PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 59": "OD1" <-> "OD2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 74": "NH1" <-> "NH2" 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: 26883 Number of models: 1 Model: "" Number of chains: 10 Chain: "2" Number of atoms: 18716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 18716 Classifications: {'RNA': 871} Modifications used: {'rna2p_pur': 68, 'rna2p_pyr': 42, 'rna3p_pur': 438, 'rna3p_pyr': 323} Link IDs: {'rna2p': 110, 'rna3p': 760} Chain breaks: 2 Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1626 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 716 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "O" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "P" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "S" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 14.09, per 1000 atoms: 0.52 Number of scatterers: 26883 At special positions: 0 Unit cell: (143.782, 187.775, 158.804, 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 33 16.00 P 871 15.00 O 7507 8.00 N 5026 7.00 C 13446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.5% alpha, 17.4% beta 298 base pairs and 466 stacking pairs defined. Time for finding SS restraints: 11.94 Creating SS restraints... Processing helix chain 'C' and resid 8 through 16 removed outlier: 3.868A pdb=" N SER C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 31 Processing helix chain 'C' and resid 49 through 66 Processing helix chain 'C' and resid 68 through 82 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.839A pdb=" N LYS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.964A pdb=" N ALA D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 146 Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'E' and resid 12 through 16 removed outlier: 5.295A pdb=" N GLU E 16 " --> pdb=" O ASP E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.501A pdb=" N GLU E 23 " --> pdb=" O PRO E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.924A pdb=" N GLU E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 21 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 94 through 99 removed outlier: 3.621A pdb=" N ALA G 97 " --> pdb=" O LYS G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'K' and resid 3 through 9 Processing helix chain 'K' and resid 113 through 118 removed outlier: 3.965A pdb=" N TYR K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 23 through 43 removed outlier: 3.699A pdb=" N ALA N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY N 40 " --> pdb=" O ASN N 36 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS N 41 " --> pdb=" O HIS N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 73 removed outlier: 3.597A pdb=" N LEU N 55 " --> pdb=" O SER N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 85 removed outlier: 4.071A pdb=" N TYR N 77 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU N 82 " --> pdb=" O THR N 78 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 63 Processing helix chain 'O' and resid 68 through 82 removed outlier: 3.517A pdb=" N ALA O 72 " --> pdb=" O SER O 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 42 removed outlier: 3.548A pdb=" N VAL S 35 " --> pdb=" O PHE S 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY S 42 " --> pdb=" O ALA S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 64 removed outlier: 3.759A pdb=" N ALA S 47 " --> pdb=" O ASP S 43 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'S' and resid 68 through 86 removed outlier: 3.616A pdb=" N ALA S 72 " --> pdb=" O HIS S 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU S 86 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.884A pdb=" N GLY C 180 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 19 removed outlier: 3.889A pdb=" N LYS D 14 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL D 38 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU D 36 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL D 18 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR D 34 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.707A pdb=" N LYS D 23 " --> pdb=" O ILE D 30 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE D 30 " --> pdb=" O LYS D 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 85 through 88 Processing sheet with id=AA5, first strand: chain 'E' and resid 40 through 45 removed outlier: 5.464A pdb=" N ASP E 41 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 61 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 43 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 57 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS E 58 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 10 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 60 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE E 8 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU E 5 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL E 89 " --> pdb=" O GLU E 5 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL E 7 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER E 87 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET E 9 " --> pdb=" O ILE E 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 24 through 28 removed outlier: 4.506A pdb=" N ASP G 48 " --> pdb=" O THR G 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 65 through 66 removed outlier: 3.547A pdb=" N PHE G 66 " --> pdb=" O LYS G 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.598A pdb=" N GLN G 76 " --> pdb=" O TYR G 128 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE G 125 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS G 127 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL G 104 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 111 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 62 through 66 removed outlier: 3.608A pdb=" N CYS K 53 " --> pdb=" O SER K 65 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ARG K 50 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR K 39 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL K 52 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL K 37 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG K 54 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 30 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 82 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 2 through 8 removed outlier: 3.728A pdb=" N GLU O 34 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'P' and resid 8 through 14 removed outlier: 8.875A pdb=" N GLN P 9 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU P 26 " --> pdb=" O GLN P 9 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL P 22 " --> pdb=" O VAL P 13 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP P 73 " --> pdb=" O HIS P 45 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU P 75 " --> pdb=" O HIS P 47 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLU P 60 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VAL P 78 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL P 58 " --> pdb=" O VAL P 78 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 754 hydrogen bonds 1214 hydrogen bond angles 0 basepair planarities 298 basepair parallelities 466 stacking parallelities Total time for adding SS restraints: 16.35 Time building geometry restraints manager: 16.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3950 1.33 - 1.45: 12379 1.45 - 1.57: 11112 1.57 - 1.69: 1739 1.69 - 1.81: 58 Bond restraints: 29238 Sorted by residual: bond pdb=" N1 U 2 287 " pdb=" C2 U 2 287 " ideal model delta sigma weight residual 1.381 1.402 -0.021 2.00e-02 2.50e+03 1.11e+00 bond pdb=" C2 C 2 613 " pdb=" O2 C 2 613 " ideal model delta sigma weight residual 1.240 1.220 0.020 2.00e-02 2.50e+03 9.98e-01 bond pdb=" CA ARG C 47 " pdb=" CB ARG C 47 " ideal model delta sigma weight residual 1.524 1.537 -0.012 1.22e-02 6.72e+03 9.92e-01 bond pdb=" C VAL E 18 " pdb=" N PRO E 19 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 9.21e-01 bond pdb=" N9 G 2 627 " pdb=" C4 G 2 627 " ideal model delta sigma weight residual 1.375 1.393 -0.018 2.00e-02 2.50e+03 7.93e-01 ... (remaining 29233 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.82: 5323 106.82 - 113.70: 17795 113.70 - 120.57: 11042 120.57 - 127.45: 7841 127.45 - 134.32: 1807 Bond angle restraints: 43808 Sorted by residual: angle pdb=" C GLU N 44 " pdb=" N HIS N 45 " pdb=" CA HIS N 45 " ideal model delta sigma weight residual 121.54 127.57 -6.03 1.91e+00 2.74e-01 9.98e+00 angle pdb=" C2' G 2 628 " pdb=" C1' G 2 628 " pdb=" N9 G 2 628 " ideal model delta sigma weight residual 112.00 116.57 -4.57 1.50e+00 4.44e-01 9.30e+00 angle pdb=" C1' U 2 287 " pdb=" N1 U 2 287 " pdb=" C2 U 2 287 " ideal model delta sigma weight residual 117.70 126.60 -8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" C ALA K 101 " pdb=" N LEU K 102 " pdb=" CA LEU K 102 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.63e+00 angle pdb=" N VAL O 36 " pdb=" CA VAL O 36 " pdb=" C VAL O 36 " ideal model delta sigma weight residual 111.62 109.37 2.25 7.90e-01 1.60e+00 8.14e+00 ... (remaining 43803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 14900 35.40 - 70.79: 621 70.79 - 106.19: 54 106.19 - 141.58: 5 141.58 - 176.97: 6 Dihedral angle restraints: 15586 sinusoidal: 12582 harmonic: 3004 Sorted by residual: dihedral pdb=" O4' U 2 439 " pdb=" C1' U 2 439 " pdb=" N1 U 2 439 " pdb=" C2 U 2 439 " ideal model delta sinusoidal sigma weight residual 200.00 40.35 159.65 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' U 2 4 " pdb=" C1' U 2 4 " pdb=" N1 U 2 4 " pdb=" C2 U 2 4 " ideal model delta sinusoidal sigma weight residual 200.00 45.13 154.87 1 1.50e+01 4.44e-03 8.13e+01 dihedral pdb=" O4' U 2 365 " pdb=" C1' U 2 365 " pdb=" N1 U 2 365 " pdb=" C2 U 2 365 " ideal model delta sinusoidal sigma weight residual 200.00 62.24 137.76 1 1.50e+01 4.44e-03 7.43e+01 ... (remaining 15583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5302 0.060 - 0.120: 279 0.120 - 0.179: 19 0.179 - 0.239: 4 0.239 - 0.299: 2 Chirality restraints: 5606 Sorted by residual: chirality pdb=" CB ILE D 106 " pdb=" CA ILE D 106 " pdb=" CG1 ILE D 106 " pdb=" CG2 ILE D 106 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1' G 2 628 " pdb=" O4' G 2 628 " pdb=" C2' G 2 628 " pdb=" N9 G 2 628 " both_signs ideal model delta sigma weight residual False 2.46 2.16 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1' C 2 754 " pdb=" O4' C 2 754 " pdb=" C2' C 2 754 " pdb=" N1 C 2 754 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 5603 not shown) Planarity restraints: 2307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 613 " -0.010 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 C 2 613 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C 2 613 " 0.051 2.00e-02 2.50e+03 pdb=" O2 C 2 613 " -0.026 2.00e-02 2.50e+03 pdb=" N3 C 2 613 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C 2 613 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C 2 613 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C 2 613 " -0.005 2.00e-02 2.50e+03 pdb=" C6 C 2 613 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 628 " 0.035 2.00e-02 2.50e+03 1.48e-02 6.58e+00 pdb=" N9 G 2 628 " -0.032 2.00e-02 2.50e+03 pdb=" C8 G 2 628 " -0.012 2.00e-02 2.50e+03 pdb=" N7 G 2 628 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 2 628 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 2 628 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G 2 628 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G 2 628 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 2 628 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G 2 628 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 628 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 2 628 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 629 " 0.030 2.00e-02 2.50e+03 1.44e-02 5.71e+00 pdb=" N9 A 2 629 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A 2 629 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 2 629 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A 2 629 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A 2 629 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A 2 629 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A 2 629 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A 2 629 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A 2 629 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A 2 629 " -0.001 2.00e-02 2.50e+03 ... (remaining 2304 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1957 2.70 - 3.25: 25511 3.25 - 3.80: 54890 3.80 - 4.35: 67062 4.35 - 4.90: 89200 Nonbonded interactions: 238620 Sorted by model distance: nonbonded pdb=" O2 U 2 49 " pdb=" N2 G 2 361 " model vdw 2.156 2.520 nonbonded pdb=" OP2 G 2 82 " pdb=" N2 G 2 82 " model vdw 2.162 2.520 nonbonded pdb=" O4 U 2 652 " pdb=" O2' G 2 752 " model vdw 2.195 2.440 nonbonded pdb=" O2 U 2 835 " pdb=" O6 G 2 851 " model vdw 2.213 2.432 nonbonded pdb=" O2' C 2 136 " pdb=" O GLY O 64 " model vdw 2.228 2.440 ... (remaining 238615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.020 Extract box with map and model: 8.300 Check model and map are aligned: 0.440 Set scattering table: 0.240 Process input model: 85.020 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.002 0.023 29238 Z= 0.114 Angle : 0.495 8.896 43808 Z= 0.265 Chirality : 0.029 0.299 5606 Planarity : 0.003 0.054 2307 Dihedral : 15.496 176.975 13646 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1029 helix: -0.94 (0.23), residues: 378 sheet: -2.67 (0.35), residues: 166 loop : -2.29 (0.25), residues: 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 272 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.4495 time to fit residues: 183.5770 Evaluate side-chains 195 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN E 52 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN O 79 ASN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 29238 Z= 0.320 Angle : 0.667 8.881 43808 Z= 0.335 Chirality : 0.036 0.297 5606 Planarity : 0.005 0.087 2307 Dihedral : 15.838 175.176 11608 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.85 (0.25), residues: 1029 helix: -0.01 (0.25), residues: 386 sheet: -2.11 (0.38), residues: 178 loop : -1.87 (0.27), residues: 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 209 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 19 residues processed: 220 average time/residue: 0.4268 time to fit residues: 143.7623 Evaluate side-chains 205 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2420 time to fit residues: 10.2150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN E 63 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 29238 Z= 0.210 Angle : 0.585 12.084 43808 Z= 0.295 Chirality : 0.033 0.286 5606 Planarity : 0.004 0.038 2307 Dihedral : 15.744 177.124 11608 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.36 (0.26), residues: 1029 helix: 0.44 (0.26), residues: 384 sheet: -1.99 (0.39), residues: 170 loop : -1.56 (0.28), residues: 475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 225 average time/residue: 0.4221 time to fit residues: 147.2398 Evaluate side-chains 193 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2781 time to fit residues: 6.1580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 7.9990 chunk 128 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 GLN O 63 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29238 Z= 0.206 Angle : 0.594 11.363 43808 Z= 0.299 Chirality : 0.033 0.286 5606 Planarity : 0.004 0.042 2307 Dihedral : 15.774 175.815 11608 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.21 (0.26), residues: 1029 helix: 0.57 (0.26), residues: 382 sheet: -1.87 (0.38), residues: 165 loop : -1.50 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 208 average time/residue: 0.4074 time to fit residues: 131.2932 Evaluate side-chains 194 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2393 time to fit residues: 7.6709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS N 27 GLN O 63 GLN P 45 HIS ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 29238 Z= 0.486 Angle : 0.847 10.882 43808 Z= 0.423 Chirality : 0.044 0.273 5606 Planarity : 0.006 0.047 2307 Dihedral : 16.703 172.723 11608 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 30.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1029 helix: 0.05 (0.25), residues: 391 sheet: -2.04 (0.37), residues: 170 loop : -1.85 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 205 average time/residue: 0.4203 time to fit residues: 132.7481 Evaluate side-chains 189 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2827 time to fit residues: 9.5065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 ASN N 27 GLN O 63 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 29238 Z= 0.241 Angle : 0.645 11.019 43808 Z= 0.326 Chirality : 0.036 0.279 5606 Planarity : 0.004 0.037 2307 Dihedral : 16.221 175.331 11608 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.40 (0.25), residues: 1029 helix: 0.36 (0.25), residues: 392 sheet: -1.91 (0.37), residues: 170 loop : -1.63 (0.27), residues: 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 207 average time/residue: 0.4306 time to fit residues: 137.2048 Evaluate side-chains 193 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2379 time to fit residues: 6.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 118 GLN N 27 GLN O 63 GLN S 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 29238 Z= 0.346 Angle : 0.709 11.769 43808 Z= 0.356 Chirality : 0.038 0.280 5606 Planarity : 0.005 0.059 2307 Dihedral : 16.306 173.963 11608 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1029 helix: 0.17 (0.25), residues: 390 sheet: -2.04 (0.36), residues: 174 loop : -1.72 (0.27), residues: 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 200 average time/residue: 0.4399 time to fit residues: 136.0073 Evaluate side-chains 191 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2598 time to fit residues: 7.1597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 29238 Z= 0.296 Angle : 0.688 14.599 43808 Z= 0.347 Chirality : 0.038 0.281 5606 Planarity : 0.005 0.036 2307 Dihedral : 16.331 174.208 11608 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.56 (0.25), residues: 1029 helix: 0.12 (0.25), residues: 393 sheet: -1.95 (0.36), residues: 179 loop : -1.61 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 195 average time/residue: 0.4211 time to fit residues: 126.1121 Evaluate side-chains 192 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2368 time to fit residues: 7.0961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 29238 Z= 0.151 Angle : 0.600 13.303 43808 Z= 0.302 Chirality : 0.033 0.285 5606 Planarity : 0.004 0.038 2307 Dihedral : 15.925 177.407 11608 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.23 (0.25), residues: 1029 helix: 0.45 (0.26), residues: 390 sheet: -1.88 (0.36), residues: 181 loop : -1.40 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 199 average time/residue: 0.4333 time to fit residues: 133.1691 Evaluate side-chains 185 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.553 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2345 time to fit residues: 4.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 29238 Z= 0.264 Angle : 0.656 14.013 43808 Z= 0.331 Chirality : 0.036 0.291 5606 Planarity : 0.005 0.100 2307 Dihedral : 15.968 175.742 11608 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.25 (0.25), residues: 1029 helix: 0.30 (0.25), residues: 390 sheet: -1.78 (0.37), residues: 172 loop : -1.35 (0.28), residues: 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 189 average time/residue: 0.4212 time to fit residues: 122.1835 Evaluate side-chains 185 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2371 time to fit residues: 3.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 ASN ** 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 = 0.3368 r_free = 0.3368 target = 0.054964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.042158 restraints weight = 193078.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.043086 restraints weight = 90190.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043336 restraints weight = 43140.801| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 29238 Z= 0.428 Angle : 0.793 13.247 43808 Z= 0.396 Chirality : 0.040 0.281 5606 Planarity : 0.006 0.059 2307 Dihedral : 16.291 172.720 11608 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.84 % Favored : 91.06 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.64 (0.25), residues: 1029 helix: 0.02 (0.25), residues: 392 sheet: -1.95 (0.37), residues: 180 loop : -1.64 (0.28), residues: 457 =============================================================================== Job complete usr+sys time: 3623.83 seconds wall clock time: 68 minutes 48.92 seconds (4128.92 seconds total)