Starting phenix.real_space_refine on Sat Mar 16 04:56:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/03_2024/8g5v_29756.pdb" } resolution = 3.0 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= 0.005 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8937 2.51 5 N 2246 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 32": "OD1" <-> "OD2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 32": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "K GLU 8": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "L ASP 22": "OD1" <-> "OD2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13739 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "A" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "D" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "G" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "E" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "K" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "J" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "L" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Time building chain proxies: 7.35, per 1000 atoms: 0.53 Number of scatterers: 13739 At special positions: 0 Unit cell: (172.78, 177.02, 72.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2484 8.00 N 2246 7.00 C 8937 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: 4.74 Conformation dependent library (CDL) restraints added in 2.6 seconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 76.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 18 through 19 No H-bonds generated for 'chain 'B' and resid 18 through 19' Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.536A pdb=" N PHE B 24 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 7.076A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 78 through 111 removed outlier: 3.831A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.668A pdb=" N VAL B 120 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.740A pdb=" N PHE A 24 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 removed outlier: 7.179A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 Processing helix chain 'A' and resid 78 through 90 removed outlier: 3.787A pdb=" N ASN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.025A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 129 through 133 Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.698A pdb=" N LEU C 16 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 44 removed outlier: 6.975A pdb=" N GLU C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 Processing helix chain 'C' and resid 78 through 111 removed outlier: 3.891A pdb=" N MET C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 44 removed outlier: 7.168A pdb=" N GLU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 Processing helix chain 'D' and resid 78 through 109 removed outlier: 3.551A pdb=" N GLY D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS D 96 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 100 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.520A pdb=" N ARG D 133 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 19 removed outlier: 3.616A pdb=" N PHE G 18 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU G 19 " --> pdb=" O LEU G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 19' Processing helix chain 'G' and resid 26 through 39 Processing helix chain 'G' and resid 49 through 75 Processing helix chain 'G' and resid 78 through 111 removed outlier: 3.750A pdb=" N GLY G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 100 " --> pdb=" O LYS G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.748A pdb=" N VAL G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 Processing helix chain 'E' and resid 26 through 44 removed outlier: 6.920A pdb=" N GLU E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 79 through 109 removed outlier: 4.278A pdb=" N ASP E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.597A pdb=" N VAL E 120 " --> pdb=" O ILE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.530A pdb=" N ARG E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 18 through 19 No H-bonds generated for 'chain 'I' and resid 18 through 19' Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.689A pdb=" N PHE I 24 " --> pdb=" O SER I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 43 removed outlier: 7.038A pdb=" N GLU I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 75 Processing helix chain 'I' and resid 78 through 111 removed outlier: 4.072A pdb=" N MET I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE I 97 " --> pdb=" O MET I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 128 Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 26 through 44 removed outlier: 7.267A pdb=" N GLU K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 Processing helix chain 'K' and resid 78 through 110 removed outlier: 3.912A pdb=" N MET K 93 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 Processing helix chain 'H' and resid 12 through 18 Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.911A pdb=" N PHE H 24 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 43 removed outlier: 6.767A pdb=" N GLU H 40 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 78 through 111 removed outlier: 3.986A pdb=" N GLY H 94 " --> pdb=" O ASN H 90 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 128 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 18 through 19 No H-bonds generated for 'chain 'F' and resid 18 through 19' Processing helix chain 'F' and resid 20 through 24 removed outlier: 4.167A pdb=" N PHE F 24 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 43 removed outlier: 7.237A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 78 through 111 removed outlier: 4.485A pdb=" N MET F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 20 through 24 removed outlier: 3.991A pdb=" N PHE J 24 " --> pdb=" O SER J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 43 removed outlier: 6.987A pdb=" N GLU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 Processing helix chain 'J' and resid 78 through 111 removed outlier: 4.589A pdb=" N MET J 93 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 Processing helix chain 'L' and resid 12 through 18 Processing helix chain 'L' and resid 20 through 24 removed outlier: 3.934A pdb=" N PHE L 24 " --> pdb=" O SER L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 44 removed outlier: 6.907A pdb=" N GLU L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 Processing helix chain 'L' and resid 78 through 110 removed outlier: 3.729A pdb=" N GLY L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS L 96 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 Processing helix chain 'L' and resid 129 through 133 946 hydrogen bonds defined for protein. 2775 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: 3.88 Time building geometry restraints manager: 5.27 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: 4332 1.34 - 1.46: 3410 1.46 - 1.58: 6315 1.58 - 1.70: 1 1.70 - 1.81: 108 Bond restraints: 14166 Sorted by residual: bond pdb=" CB PRO L 45 " pdb=" CG PRO L 45 " ideal model delta sigma weight residual 1.492 1.624 -0.132 5.00e-02 4.00e+02 6.96e+00 bond pdb=" CG1 ILE H 59 " pdb=" CD1 ILE H 59 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CB VAL E 115 " pdb=" CG2 VAL E 115 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CG PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.20e+00 bond pdb=" CG1 ILE E 126 " pdb=" CD1 ILE E 126 " ideal model delta sigma weight residual 1.513 1.474 0.039 3.90e-02 6.57e+02 1.03e+00 ... (remaining 14161 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.36: 336 104.36 - 111.78: 6959 111.78 - 119.20: 4621 119.20 - 126.62: 7123 126.62 - 134.04: 360 Bond angle restraints: 19399 Sorted by residual: angle pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" CD PRO L 45 " ideal model delta sigma weight residual 112.00 101.92 10.08 1.40e+00 5.10e-01 5.18e+01 angle pdb=" C LEU D 60 " pdb=" N CYS D 61 " pdb=" CA CYS D 61 " ideal model delta sigma weight residual 121.14 115.79 5.35 1.75e+00 3.27e-01 9.34e+00 angle pdb=" CB MET B 66 " pdb=" CG MET B 66 " pdb=" SD MET B 66 " ideal model delta sigma weight residual 112.70 103.90 8.80 3.00e+00 1.11e-01 8.61e+00 angle pdb=" C LEU C 60 " pdb=" N CYS C 61 " pdb=" CA CYS C 61 " ideal model delta sigma weight residual 121.14 116.12 5.02 1.75e+00 3.27e-01 8.21e+00 angle pdb=" C ASN B 75 " pdb=" N LEU B 76 " pdb=" CA LEU B 76 " ideal model delta sigma weight residual 122.64 118.29 4.35 1.70e+00 3.46e-01 6.55e+00 ... (remaining 19394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 7590 17.22 - 34.43: 628 34.43 - 51.65: 107 51.65 - 68.87: 20 68.87 - 86.08: 2 Dihedral angle restraints: 8347 sinusoidal: 3289 harmonic: 5058 Sorted by residual: dihedral pdb=" CA PHE C 24 " pdb=" C PHE C 24 " pdb=" N PRO C 25 " pdb=" CA PRO C 25 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU E 108 " pdb=" C LEU E 108 " pdb=" N THR E 109 " pdb=" CA THR E 109 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA LEU G 76 " pdb=" C LEU G 76 " pdb=" N GLU G 77 " pdb=" CA GLU G 77 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1199 0.027 - 0.055: 626 0.055 - 0.082: 241 0.082 - 0.109: 107 0.109 - 0.137: 20 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CG LEU D 55 " pdb=" CB LEU D 55 " pdb=" CD1 LEU D 55 " pdb=" CD2 LEU D 55 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" C PRO L 45 " pdb=" CB PRO L 45 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA LYS L 96 " pdb=" N LYS L 96 " pdb=" C LYS L 96 " pdb=" CB LYS L 96 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2190 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 44 " -0.056 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO L 45 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 71 " 0.015 2.00e-02 2.50e+03 1.65e-02 6.82e+00 pdb=" CG TRP B 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 71 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 71 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 71 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 71 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 71 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 71 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 18 " -0.018 2.00e-02 2.50e+03 1.71e-02 5.10e+00 pdb=" CG PHE E 18 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 18 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 18 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 18 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE E 18 " -0.001 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2385 2.76 - 3.29: 13441 3.29 - 3.83: 24258 3.83 - 4.36: 27985 4.36 - 4.90: 48728 Nonbonded interactions: 116797 Sorted by model distance: nonbonded pdb=" OE1 GLU J 8 " pdb=" NH1 ARG L 56 " model vdw 2.223 2.520 nonbonded pdb=" NH1 ARG H 56 " pdb=" OE1 GLU F 8 " model vdw 2.232 2.520 nonbonded pdb=" NH1 ARG G 56 " pdb=" OE1 GLU E 8 " model vdw 2.256 2.520 nonbonded pdb=" OG SER D 49 " pdb=" ND1 HIS D 52 " model vdw 2.286 2.520 nonbonded pdb=" O GLU D 64 " pdb=" OG1 THR D 67 " model vdw 2.302 2.440 ... (remaining 116792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 141) selection = (chain 'D' and resid 1 through 141) selection = (chain 'E' and resid 1 through 141) selection = (chain 'F' and resid 1 through 141) selection = (chain 'G' and resid 1 through 141) selection = (chain 'H' and resid 1 through 141) selection = (chain 'I' and resid 1 through 141) selection = (chain 'J' and resid 1 through 141) selection = (chain 'K' and resid 1 through 141) selection = (chain 'L' and resid 1 through 141) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.830 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.690 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.050 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:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2364 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 0.132 14166 Z= 0.250 Angle : 0.609 10.080 19399 Z= 0.313 Chirality : 0.040 0.137 2193 Planarity : 0.005 0.079 2457 Dihedral : 12.944 86.081 5055 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.21), residues: 1694 helix: 1.65 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : 1.12 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 71 HIS 0.006 0.001 HIS A 104 PHE 0.039 0.002 PHE E 18 TYR 0.017 0.002 TYR A 88 ARG 0.003 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.718 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: C 66 MET cc_start: 0.6091 (mmm) cc_final: 0.5362 (mmp) REVERT: D 72 VAL cc_start: 0.4246 (t) cc_final: 0.3981 (p) REVERT: F 93 MET cc_start: 0.1301 (mmt) cc_final: 0.0428 (mtt) outliers start: 0 outliers final: 2 residues processed: 301 average time/residue: 0.9011 time to fit residues: 307.4622 Evaluate side-chains 157 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain J residue 47 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.8980 chunk 127 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS G 47 HIS K 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2928 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14166 Z= 0.193 Angle : 0.652 10.886 19399 Z= 0.318 Chirality : 0.039 0.307 2193 Planarity : 0.005 0.064 2457 Dihedral : 4.181 19.580 1866 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.36 % Allowed : 9.24 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.21), residues: 1694 helix: 1.34 (0.15), residues: 1266 sheet: None (None), residues: 0 loop : 0.85 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 71 HIS 0.009 0.001 HIS A 51 PHE 0.022 0.002 PHE B 24 TYR 0.019 0.001 TYR E 88 ARG 0.009 0.001 ARG I 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ARG cc_start: 0.5654 (ttm110) cc_final: 0.5428 (ttp80) REVERT: G 51 HIS cc_start: 0.6250 (m-70) cc_final: 0.5967 (m-70) REVERT: G 66 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6754 (mpp) REVERT: G 77 GLU cc_start: 0.5422 (mm-30) cc_final: 0.5168 (mm-30) REVERT: E 40 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: I 68 LEU cc_start: 0.4542 (tp) cc_final: 0.4149 (tm) REVERT: K 66 MET cc_start: 0.5653 (mmp) cc_final: 0.5176 (mmp) REVERT: H 1 MET cc_start: 0.0154 (tpp) cc_final: -0.1302 (ttp) REVERT: H 93 MET cc_start: 0.4820 (mmp) cc_final: 0.4585 (mmp) REVERT: F 1 MET cc_start: 0.0749 (ttm) cc_final: -0.0087 (pmm) REVERT: F 93 MET cc_start: 0.1230 (mmt) cc_final: 0.0444 (mtt) REVERT: L 82 ARG cc_start: 0.4854 (ttp80) cc_final: 0.4454 (ttp-170) outliers start: 36 outliers final: 11 residues processed: 199 average time/residue: 0.7843 time to fit residues: 179.3214 Evaluate side-chains 158 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain K residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 165 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN K 51 HIS J 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3196 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14166 Z= 0.180 Angle : 0.625 10.276 19399 Z= 0.301 Chirality : 0.040 0.368 2193 Planarity : 0.005 0.096 2457 Dihedral : 4.063 20.458 1862 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.82 % Allowed : 11.53 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1694 helix: 1.35 (0.15), residues: 1267 sheet: None (None), residues: 0 loop : 1.05 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 62 HIS 0.008 0.001 HIS E 47 PHE 0.025 0.001 PHE A 122 TYR 0.020 0.001 TYR F 6 ARG 0.014 0.000 ARG G 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: K 66 MET cc_start: 0.6100 (mmp) cc_final: 0.5663 (mmp) REVERT: F 1 MET cc_start: 0.0729 (ttm) cc_final: -0.0378 (pmm) REVERT: F 93 MET cc_start: 0.1245 (mmt) cc_final: 0.0429 (mtt) REVERT: L 82 ARG cc_start: 0.4896 (ttp80) cc_final: 0.4082 (mtp180) outliers start: 43 outliers final: 13 residues processed: 187 average time/residue: 0.8297 time to fit residues: 176.3231 Evaluate side-chains 154 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 78 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN C 92 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 HIS H 47 HIS F 136 ASN L 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4486 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 14166 Z= 0.317 Angle : 0.800 20.986 19399 Z= 0.403 Chirality : 0.047 0.532 2193 Planarity : 0.006 0.072 2457 Dihedral : 4.439 25.892 1862 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.48 % Favored : 97.46 % Rotamer: Outliers : 4.00 % Allowed : 13.37 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1694 helix: 0.97 (0.14), residues: 1256 sheet: None (None), residues: 0 loop : 0.79 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 62 HIS 0.009 0.002 HIS K 51 PHE 0.046 0.003 PHE F 24 TYR 0.048 0.003 TYR C 6 ARG 0.038 0.001 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 222 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ARG cc_start: 0.6516 (ttm110) cc_final: 0.6297 (ttp80) REVERT: D 42 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7023 (mt) REVERT: E 29 ASP cc_start: 0.7470 (m-30) cc_final: 0.7184 (m-30) REVERT: E 40 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: E 90 ASN cc_start: 0.7928 (m-40) cc_final: 0.7606 (m-40) REVERT: I 67 THR cc_start: 0.3087 (OUTLIER) cc_final: 0.2806 (t) REVERT: H 1 MET cc_start: 0.0791 (tpp) cc_final: -0.0210 (tpp) REVERT: F 1 MET cc_start: 0.0870 (ttm) cc_final: -0.0113 (pmm) REVERT: F 93 MET cc_start: 0.1481 (mmt) cc_final: 0.0695 (mtt) REVERT: L 82 ARG cc_start: 0.5015 (ttp80) cc_final: 0.4439 (ttp-170) outliers start: 61 outliers final: 16 residues processed: 255 average time/residue: 0.8629 time to fit residues: 248.8035 Evaluate side-chains 180 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.0270 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 0.0980 chunk 145 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS D 57 GLN E 47 HIS ** I 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.8738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 14166 Z= 0.335 Angle : 0.867 15.864 19399 Z= 0.414 Chirality : 0.047 0.552 2193 Planarity : 0.007 0.144 2457 Dihedral : 4.544 26.577 1862 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 4.65 % Allowed : 16.19 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1694 helix: 0.97 (0.15), residues: 1213 sheet: None (None), residues: 0 loop : 0.88 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 102 HIS 0.014 0.002 HIS K 104 PHE 0.030 0.003 PHE C 24 TYR 0.034 0.002 TYR F 118 ARG 0.016 0.001 ARG G 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 238 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.4733 (tt0) cc_final: 0.4043 (mm-30) REVERT: C 60 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7333 (mp) REVERT: D 93 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5145 (mtp) REVERT: G 12 THR cc_start: 0.8783 (p) cc_final: 0.8556 (t) REVERT: G 29 ASP cc_start: 0.7211 (m-30) cc_final: 0.6922 (m-30) REVERT: G 116 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7872 (mm) REVERT: G 120 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7963 (t) REVERT: G 124 VAL cc_start: 0.7705 (p) cc_final: 0.7444 (m) REVERT: K 1 MET cc_start: 0.5107 (tmt) cc_final: 0.4630 (tmt) REVERT: K 62 TRP cc_start: 0.6925 (OUTLIER) cc_final: 0.5268 (t60) REVERT: K 136 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7174 (m-40) REVERT: F 1 MET cc_start: 0.1242 (ttm) cc_final: -0.0291 (pmm) REVERT: F 93 MET cc_start: 0.1809 (mmt) cc_final: 0.1367 (ptp) REVERT: L 82 ARG cc_start: 0.5080 (ttp80) cc_final: 0.4810 (ttp-170) outliers start: 71 outliers final: 16 residues processed: 277 average time/residue: 0.9201 time to fit residues: 286.5233 Evaluate side-chains 206 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 184 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 62 TRP Chi-restraints excluded: chain K residue 136 ASN Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain L residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 1.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14166 Z= 0.295 Angle : 0.790 13.121 19399 Z= 0.393 Chirality : 0.047 0.309 2193 Planarity : 0.006 0.068 2457 Dihedral : 4.669 24.969 1862 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % Rotamer: Outliers : 3.80 % Allowed : 18.35 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1694 helix: 0.95 (0.14), residues: 1216 sheet: None (None), residues: 0 loop : 0.75 (0.31), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 102 HIS 0.026 0.002 HIS L 52 PHE 0.041 0.003 PHE F 122 TYR 0.029 0.003 TYR J 118 ARG 0.011 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 255 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.1841 (OUTLIER) cc_final: 0.1450 (tm-30) REVERT: C 60 LEU cc_start: 0.7926 (mm) cc_final: 0.7576 (mt) REVERT: D 14 GLU cc_start: 0.4337 (OUTLIER) cc_final: 0.3469 (mp0) REVERT: G 29 ASP cc_start: 0.7115 (m-30) cc_final: 0.6868 (m-30) REVERT: G 30 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7933 (mt) REVERT: G 82 ARG cc_start: 0.5380 (tpp80) cc_final: 0.5178 (tpp-160) REVERT: E 93 MET cc_start: 0.6751 (mpm) cc_final: 0.6551 (mpt) REVERT: I 1 MET cc_start: 0.6436 (ttt) cc_final: 0.6104 (ttt) REVERT: I 52 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7502 (m90) REVERT: K 62 TRP cc_start: 0.7247 (OUTLIER) cc_final: 0.5069 (t60) REVERT: F 132 TYR cc_start: -0.0213 (OUTLIER) cc_final: -0.2906 (m-10) REVERT: J 112 ARG cc_start: 0.6961 (tmm-80) cc_final: 0.6501 (ttt180) REVERT: L 82 ARG cc_start: 0.5094 (ttp80) cc_final: 0.4824 (ttp-170) outliers start: 58 outliers final: 13 residues processed: 292 average time/residue: 1.1201 time to fit residues: 361.0291 Evaluate side-chains 222 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 52 HIS Chi-restraints excluded: chain K residue 62 TRP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain F residue 132 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 HIS ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 1.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14166 Z= 0.272 Angle : 0.759 12.644 19399 Z= 0.371 Chirality : 0.044 0.365 2193 Planarity : 0.006 0.051 2457 Dihedral : 4.451 24.721 1862 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 3.93 % Allowed : 20.84 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1694 helix: 1.19 (0.15), residues: 1227 sheet: None (None), residues: 0 loop : 1.01 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 62 HIS 0.010 0.002 HIS L 52 PHE 0.029 0.002 PHE C 24 TYR 0.018 0.002 TYR C 88 ARG 0.006 0.001 ARG H 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 244 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6928 (ttt) cc_final: 0.6605 (ttt) REVERT: C 60 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7596 (mt) REVERT: D 14 GLU cc_start: 0.4243 (OUTLIER) cc_final: 0.3768 (mp0) REVERT: G 117 GLU cc_start: 0.7515 (pt0) cc_final: 0.7218 (pt0) REVERT: E 40 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: K 83 ASP cc_start: 0.7754 (t0) cc_final: 0.7280 (m-30) REVERT: H 66 MET cc_start: 0.3576 (OUTLIER) cc_final: 0.2860 (ptp) REVERT: J 1 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.3062 (ttp) REVERT: J 112 ARG cc_start: 0.7407 (tmm-80) cc_final: 0.7193 (ttm170) REVERT: L 18 PHE cc_start: -0.0052 (OUTLIER) cc_final: -0.2063 (m-10) outliers start: 60 outliers final: 15 residues processed: 283 average time/residue: 1.1283 time to fit residues: 351.7925 Evaluate side-chains 228 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN H 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 1.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14166 Z= 0.218 Angle : 0.708 15.761 19399 Z= 0.341 Chirality : 0.041 0.295 2193 Planarity : 0.005 0.062 2457 Dihedral : 4.335 25.838 1862 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 24.25 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1694 helix: 1.27 (0.15), residues: 1233 sheet: None (None), residues: 0 loop : 1.10 (0.32), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 71 HIS 0.010 0.001 HIS F 51 PHE 0.022 0.002 PHE C 24 TYR 0.016 0.001 TYR H 132 ARG 0.005 0.001 ARG J 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.597 Fit side-chains revert: symmetry clash REVERT: B 12 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7890 (p) REVERT: B 96 LYS cc_start: 0.7097 (mttp) cc_final: 0.6839 (mptt) REVERT: A 132 TYR cc_start: 0.3363 (m-80) cc_final: 0.2551 (t80) REVERT: C 1 MET cc_start: 0.7300 (ttt) cc_final: 0.6852 (ttp) REVERT: C 46 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6771 (pp20) REVERT: C 66 MET cc_start: 0.7536 (mmm) cc_final: 0.7287 (mmp) REVERT: D 14 GLU cc_start: 0.4226 (OUTLIER) cc_final: 0.3765 (mp0) REVERT: D 93 MET cc_start: 0.6694 (mtm) cc_final: 0.6405 (mtm) REVERT: D 117 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7130 (tm-30) REVERT: G 82 ARG cc_start: 0.5842 (tpp-160) cc_final: 0.5582 (tpp-160) REVERT: G 117 GLU cc_start: 0.7450 (pt0) cc_final: 0.7153 (pt0) REVERT: I 93 MET cc_start: 0.6217 (tmm) cc_final: 0.5881 (ppp) REVERT: K 83 ASP cc_start: 0.7818 (t0) cc_final: 0.7328 (m-30) REVERT: H 66 MET cc_start: 0.3822 (mmp) cc_final: 0.2824 (ptp) REVERT: J 1 MET cc_start: 0.4620 (OUTLIER) cc_final: 0.3652 (ttt) REVERT: J 93 MET cc_start: 0.4956 (mmm) cc_final: 0.4503 (mpp) REVERT: J 112 ARG cc_start: 0.7491 (tmm-80) cc_final: 0.7268 (ttp80) REVERT: L 18 PHE cc_start: 0.0144 (OUTLIER) cc_final: -0.1872 (m-10) outliers start: 27 outliers final: 10 residues processed: 246 average time/residue: 1.2497 time to fit residues: 335.6171 Evaluate side-chains 216 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 150 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN F 51 HIS J 47 HIS J 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 1.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14166 Z= 0.190 Angle : 0.686 14.636 19399 Z= 0.330 Chirality : 0.040 0.294 2193 Planarity : 0.005 0.047 2457 Dihedral : 4.187 24.946 1862 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.24 % Favored : 97.70 % Rotamer: Outliers : 1.77 % Allowed : 25.82 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1694 helix: 1.23 (0.15), residues: 1265 sheet: None (None), residues: 0 loop : 0.96 (0.33), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 71 HIS 0.005 0.001 HIS F 51 PHE 0.022 0.002 PHE F 9 TYR 0.020 0.001 TYR D 88 ARG 0.010 0.001 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 LYS cc_start: 0.7241 (mttp) cc_final: 0.6984 (mptt) REVERT: A 14 GLU cc_start: 0.2078 (OUTLIER) cc_final: 0.0029 (pp20) REVERT: C 46 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6806 (pp20) REVERT: D 14 GLU cc_start: 0.4429 (OUTLIER) cc_final: 0.4065 (mp0) REVERT: G 82 ARG cc_start: 0.6111 (tpp-160) cc_final: 0.5807 (tpp-160) REVERT: G 117 GLU cc_start: 0.7430 (pt0) cc_final: 0.7138 (pt0) REVERT: E 40 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: K 83 ASP cc_start: 0.7819 (t0) cc_final: 0.7360 (m-30) REVERT: K 87 SER cc_start: 0.8023 (t) cc_final: 0.7744 (p) REVERT: H 66 MET cc_start: 0.3849 (mmp) cc_final: 0.3008 (ptp) REVERT: H 93 MET cc_start: 0.5744 (mpm) cc_final: 0.5439 (mpt) REVERT: F 93 MET cc_start: 0.4812 (pmm) cc_final: 0.2694 (mpp) REVERT: J 1 MET cc_start: 0.4628 (OUTLIER) cc_final: 0.3801 (ttt) REVERT: J 93 MET cc_start: 0.4889 (mmm) cc_final: 0.3942 (mpp) REVERT: L 18 PHE cc_start: 0.0040 (OUTLIER) cc_final: -0.1989 (m-10) outliers start: 27 outliers final: 8 residues processed: 242 average time/residue: 1.1987 time to fit residues: 317.4272 Evaluate side-chains 218 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 136 ASN Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 0.0970 chunk 133 optimal weight: 10.0000 chunk 13 optimal weight: 0.0020 chunk 102 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN F 104 HIS J 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 1.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14166 Z= 0.179 Angle : 0.674 13.079 19399 Z= 0.325 Chirality : 0.040 0.296 2193 Planarity : 0.005 0.050 2457 Dihedral : 4.123 24.126 1862 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.18 % Allowed : 26.28 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1694 helix: 1.27 (0.15), residues: 1261 sheet: None (None), residues: 0 loop : 0.95 (0.33), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 71 HIS 0.007 0.001 HIS F 51 PHE 0.014 0.001 PHE C 24 TYR 0.022 0.001 TYR D 88 ARG 0.015 0.001 ARG B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 VAL cc_start: 0.8380 (p) cc_final: 0.8158 (t) REVERT: B 96 LYS cc_start: 0.7351 (mttp) cc_final: 0.7067 (mptt) REVERT: C 60 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7867 (mt) REVERT: C 66 MET cc_start: 0.7700 (mmm) cc_final: 0.7468 (mmp) REVERT: D 14 GLU cc_start: 0.4390 (OUTLIER) cc_final: 0.4064 (mp0) REVERT: G 7 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7712 (tppt) REVERT: G 82 ARG cc_start: 0.6023 (tpp-160) cc_final: 0.5715 (tpp-160) REVERT: G 117 GLU cc_start: 0.7429 (pt0) cc_final: 0.7117 (pt0) REVERT: E 66 MET cc_start: 0.7614 (mmm) cc_final: 0.6838 (mmp) REVERT: I 66 MET cc_start: 0.6222 (tpt) cc_final: 0.5765 (tpp) REVERT: K 1 MET cc_start: 0.5336 (tmt) cc_final: 0.4735 (ttt) REVERT: K 60 LEU cc_start: 0.8142 (mt) cc_final: 0.7937 (mt) REVERT: K 83 ASP cc_start: 0.7825 (t0) cc_final: 0.7385 (m-30) REVERT: K 87 SER cc_start: 0.8101 (t) cc_final: 0.7848 (p) REVERT: H 66 MET cc_start: 0.4011 (mmp) cc_final: 0.2918 (ptp) REVERT: H 93 MET cc_start: 0.5686 (mpm) cc_final: 0.5437 (mpt) REVERT: F 93 MET cc_start: 0.4903 (pmm) cc_final: 0.2561 (mpp) REVERT: J 1 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.3737 (ttp) REVERT: J 93 MET cc_start: 0.5054 (mmm) cc_final: 0.4234 (mpp) REVERT: L 18 PHE cc_start: 0.0143 (OUTLIER) cc_final: -0.1918 (m-10) outliers start: 18 outliers final: 9 residues processed: 232 average time/residue: 1.1662 time to fit residues: 296.7100 Evaluate side-chains 223 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 136 ASN Chi-restraints excluded: chain L residue 18 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 133 optimal weight: 0.0070 chunk 55 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.146393 restraints weight = 22930.863| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.75 r_work: 0.3828 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 1.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14166 Z= 0.171 Angle : 0.671 12.835 19399 Z= 0.321 Chirality : 0.040 0.286 2193 Planarity : 0.005 0.046 2457 Dihedral : 4.044 22.560 1862 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.25 % Allowed : 26.67 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.21), residues: 1694 helix: 1.33 (0.15), residues: 1264 sheet: None (None), residues: 0 loop : 0.95 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 71 HIS 0.009 0.001 HIS B 47 PHE 0.014 0.001 PHE C 24 TYR 0.024 0.001 TYR D 88 ARG 0.005 0.000 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.56 seconds wall clock time: 94 minutes 55.91 seconds (5695.91 seconds total)