Starting phenix.real_space_refine on Sun Nov 17 10:17:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/11_2024/8g5v_29756.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/11_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_29756/11_2024/8g5v_29756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/11_2024/8g5v_29756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/11_2024/8g5v_29756.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g5v_29756/11_2024/8g5v_29756.cif" } 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. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.44, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 3.28 Conformation dependent library (CDL) restraints added in 1.6 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: 1.01 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: 3.85 Time building geometry restraints manager: 3.84 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: 0.00 - 2.02: 19053 2.02 - 4.03: 307 4.03 - 6.05: 32 6.05 - 8.06: 3 8.06 - 10.08: 4 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 3.120 nonbonded pdb=" NH1 ARG H 56 " pdb=" OE1 GLU F 8 " model vdw 2.232 3.120 nonbonded pdb=" NH1 ARG G 56 " pdb=" OE1 GLU E 8 " model vdw 2.256 3.120 nonbonded pdb=" OG SER D 49 " pdb=" ND1 HIS D 52 " model vdw 2.286 3.120 nonbonded pdb=" O GLU D 64 " pdb=" OG1 THR D 67 " model vdw 2.302 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 19.050 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.440 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.040 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.547 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: 0.9330 time to fit residues: 318.3255 Evaluate side-chains 157 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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: 1.9990 chunk 127 optimal weight: 0.0970 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 HIS G 47 HIS K 47 HIS K 90 ASN K 104 HIS F 136 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3190 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14166 Z= 0.233 Angle : 0.692 11.805 19399 Z= 0.342 Chirality : 0.041 0.329 2193 Planarity : 0.006 0.066 2457 Dihedral : 4.324 21.603 1866 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.62 % Allowed : 9.31 % Favored : 88.07 % 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: 1.45 (0.20), residues: 1694 helix: 1.12 (0.14), residues: 1267 sheet: None (None), residues: 0 loop : 0.83 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 71 HIS 0.010 0.002 HIS K 51 PHE 0.021 0.002 PHE A 122 TYR 0.022 0.002 TYR E 88 ARG 0.010 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 229 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3165 (tt0) cc_final: 0.2463 (mm-30) REVERT: G 66 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6912 (mpp) REVERT: E 40 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: I 68 LEU cc_start: 0.4567 (tp) cc_final: 0.4162 (tm) REVERT: I 78 ASP cc_start: 0.4706 (m-30) cc_final: 0.3858 (t0) REVERT: K 66 MET cc_start: 0.5910 (mmp) cc_final: 0.5337 (mmp) REVERT: H 1 MET cc_start: 0.0431 (tpp) cc_final: -0.0097 (ttp) REVERT: H 93 MET cc_start: 0.4827 (mmp) cc_final: 0.4576 (mmp) REVERT: F 1 MET cc_start: 0.0571 (ttm) cc_final: -0.0056 (pmm) REVERT: F 93 MET cc_start: 0.1460 (mmt) cc_final: 0.0717 (mtt) REVERT: L 82 ARG cc_start: 0.4768 (ttp80) cc_final: 0.4455 (ttp-170) outliers start: 40 outliers final: 13 residues processed: 208 average time/residue: 0.8929 time to fit residues: 210.8158 Evaluate side-chains 169 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 2 ASP Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain I residue 82 ARG Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3484 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14166 Z= 0.192 Angle : 0.629 9.874 19399 Z= 0.307 Chirality : 0.041 0.359 2193 Planarity : 0.005 0.066 2457 Dihedral : 4.085 16.420 1862 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.01 % Allowed : 11.86 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1694 helix: 1.25 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.96 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 62 HIS 0.004 0.001 HIS J 47 PHE 0.027 0.002 PHE F 24 TYR 0.033 0.001 TYR F 118 ARG 0.012 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 222 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3563 (tt0) cc_final: 0.2712 (mm-30) REVERT: E 40 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: K 66 MET cc_start: 0.6109 (mmp) cc_final: 0.5679 (mmp) REVERT: H 1 MET cc_start: 0.0311 (tpp) cc_final: -0.1065 (ttp) REVERT: F 1 MET cc_start: 0.0766 (ttm) cc_final: -0.0072 (pmm) REVERT: F 93 MET cc_start: 0.1418 (mmt) cc_final: 0.0588 (mtt) REVERT: L 82 ARG cc_start: 0.4919 (ttp80) cc_final: 0.4632 (ttp-110) outliers start: 46 outliers final: 11 residues processed: 200 average time/residue: 0.8918 time to fit residues: 202.2704 Evaluate side-chains 156 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 85 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 119 LEU Chi-restraints excluded: chain H residue 19 LEU 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: 6.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS F 52 HIS L 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4104 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14166 Z= 0.225 Angle : 0.685 13.731 19399 Z= 0.337 Chirality : 0.042 0.423 2193 Planarity : 0.005 0.071 2457 Dihedral : 4.095 17.305 1862 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Rotamer: Outliers : 3.67 % Allowed : 12.71 % Favored : 83.62 % 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: 1.68 (0.20), residues: 1694 helix: 1.26 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 1.03 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 62 HIS 0.005 0.001 HIS B 52 PHE 0.018 0.002 PHE K 18 TYR 0.017 0.002 TYR I 88 ARG 0.013 0.001 ARG B 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 253 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.3531 (tt0) cc_final: 0.3023 (mm-30) REVERT: C 14 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.5081 (tt0) REVERT: C 112 ARG cc_start: 0.6500 (ttm110) cc_final: 0.6201 (ttp80) REVERT: D 42 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6724 (mt) REVERT: E 29 ASP cc_start: 0.7174 (m-30) cc_final: 0.6955 (m-30) REVERT: E 90 ASN cc_start: 0.7885 (m-40) cc_final: 0.7569 (m-40) REVERT: K 66 MET cc_start: 0.5974 (mmp) cc_final: 0.5684 (mmp) REVERT: F 1 MET cc_start: 0.1027 (ttm) cc_final: 0.0153 (pmm) REVERT: F 93 MET cc_start: 0.1373 (mmt) cc_final: 0.0612 (mtt) REVERT: J 1 MET cc_start: 0.2277 (OUTLIER) cc_final: 0.2048 (mmm) REVERT: L 82 ARG cc_start: 0.4872 (ttp80) cc_final: 0.4310 (ttp80) outliers start: 56 outliers final: 19 residues processed: 222 average time/residue: 0.9053 time to fit residues: 227.4893 Evaluate side-chains 174 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.472 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain J residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 HIS ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 52 HIS ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 1.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 14166 Z= 0.478 Angle : 1.097 17.612 19399 Z= 0.561 Chirality : 0.059 0.644 2193 Planarity : 0.009 0.089 2457 Dihedral : 5.989 37.689 1862 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 4.98 % Allowed : 15.40 % Favored : 79.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1694 helix: -0.04 (0.14), residues: 1206 sheet: None (None), residues: 0 loop : -0.12 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP K 62 HIS 0.015 0.004 HIS A 52 PHE 0.056 0.005 PHE C 23 TYR 0.034 0.004 TYR K 6 ARG 0.026 0.001 ARG B 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 362 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 286 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.1652 (OUTLIER) cc_final: 0.1263 (tm-30) REVERT: A 132 TYR cc_start: 0.3645 (m-80) cc_final: 0.3153 (t80) REVERT: C 14 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: D 12 THR cc_start: 0.8557 (p) cc_final: 0.8299 (t) REVERT: D 14 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.4050 (mp0) REVERT: G 7 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8040 (ttmt) REVERT: G 12 THR cc_start: 0.9021 (p) cc_final: 0.8749 (t) REVERT: G 117 GLU cc_start: 0.7600 (pt0) cc_final: 0.7275 (pt0) REVERT: I 52 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.7531 (m90) REVERT: K 12 THR cc_start: 0.8274 (p) cc_final: 0.7608 (p) REVERT: K 85 VAL cc_start: 0.8402 (t) cc_final: 0.8175 (m) REVERT: F 1 MET cc_start: 0.1600 (ttm) cc_final: 0.0350 (pmm) REVERT: F 93 MET cc_start: 0.2647 (mmt) cc_final: 0.2396 (ptp) REVERT: F 132 TYR cc_start: -0.0021 (OUTLIER) cc_final: -0.1284 (m-80) REVERT: L 18 PHE cc_start: 0.0322 (OUTLIER) cc_final: -0.1965 (m-10) REVERT: L 82 ARG cc_start: 0.5118 (ttp80) cc_final: 0.4216 (mtp180) outliers start: 76 outliers final: 17 residues processed: 334 average time/residue: 1.2195 time to fit residues: 447.4926 Evaluate side-chains 223 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 120 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 I residue 67 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 132 TYR Chi-restraints excluded: chain L residue 18 PHE Chi-restraints excluded: chain L residue 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS C 104 HIS E 47 HIS ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 GLN ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 1.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14166 Z= 0.220 Angle : 0.699 12.463 19399 Z= 0.350 Chirality : 0.042 0.280 2193 Planarity : 0.005 0.056 2457 Dihedral : 4.772 21.936 1862 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.83 % Favored : 98.11 % Rotamer: Outliers : 3.08 % Allowed : 19.92 % Favored : 77.00 % 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: 1.00 (0.20), residues: 1694 helix: 0.83 (0.14), residues: 1231 sheet: None (None), residues: 0 loop : 0.54 (0.32), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 71 HIS 0.031 0.002 HIS F 52 PHE 0.019 0.002 PHE G 97 TYR 0.015 0.002 TYR H 132 ARG 0.004 0.001 ARG C 112 *********************** 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 268 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: B 39 ARG cc_start: 0.7035 (ttt-90) cc_final: 0.6800 (ttm-80) REVERT: A 132 TYR cc_start: 0.3373 (m-80) cc_final: 0.2887 (t80) REVERT: G 7 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7869 (ttmt) REVERT: G 39 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7637 (ttp80) REVERT: G 117 GLU cc_start: 0.7475 (pt0) cc_final: 0.7157 (pt0) REVERT: K 46 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: K 65 LEU cc_start: 0.6856 (tt) cc_final: 0.6407 (mm) REVERT: K 143 LEU cc_start: 0.6545 (tp) cc_final: 0.5885 (tp) REVERT: F 1 MET cc_start: 0.1774 (ttm) cc_final: 0.1039 (pmm) REVERT: J 1 MET cc_start: 0.3564 (tmm) cc_final: 0.3008 (ttp) REVERT: L 82 ARG cc_start: 0.4846 (ttp80) cc_final: 0.4609 (ttp-170) outliers start: 47 outliers final: 13 residues processed: 257 average time/residue: 1.2998 time to fit residues: 366.5250 Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain F residue 72 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 0.0870 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 0.0020 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 52 HIS ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 HIS ** H 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 1.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14166 Z= 0.189 Angle : 0.669 13.128 19399 Z= 0.324 Chirality : 0.041 0.332 2193 Planarity : 0.005 0.117 2457 Dihedral : 4.365 19.123 1862 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 21.23 % Favored : 76.28 % 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: 1.49 (0.21), residues: 1694 helix: 1.17 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : 0.79 (0.32), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 71 HIS 0.013 0.001 HIS F 51 PHE 0.016 0.001 PHE G 97 TYR 0.012 0.001 TYR H 132 ARG 0.012 0.001 ARG G 82 *********************** 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 254 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: B 12 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6913 (p) REVERT: A 66 MET cc_start: 0.2652 (mpm) cc_final: 0.2376 (mmt) REVERT: C 95 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7555 (tt) REVERT: G 7 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7860 (ttmt) REVERT: G 117 GLU cc_start: 0.7332 (pt0) cc_final: 0.7004 (pt0) REVERT: K 85 VAL cc_start: 0.8156 (t) cc_final: 0.7870 (m) REVERT: H 66 MET cc_start: 0.2937 (mmp) cc_final: 0.2062 (ptp) REVERT: H 93 MET cc_start: 0.4755 (mmp) cc_final: 0.3819 (mpp) REVERT: F 1 MET cc_start: 0.1659 (ttm) cc_final: 0.1139 (pmm) REVERT: F 122 PHE cc_start: 0.4061 (OUTLIER) cc_final: 0.3221 (m-80) REVERT: J 93 MET cc_start: 0.4430 (mmm) cc_final: 0.2549 (tmt) outliers start: 38 outliers final: 14 residues processed: 242 average time/residue: 1.1820 time to fit residues: 315.0037 Evaluate side-chains 213 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain D residue 1 MET 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 67 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain J residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 47 HIS E 92 ASN K 51 HIS K 104 HIS F 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 1.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 14166 Z= 0.348 Angle : 0.870 12.771 19399 Z= 0.443 Chirality : 0.048 0.365 2193 Planarity : 0.007 0.101 2457 Dihedral : 4.962 20.492 1862 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 2.69 % Allowed : 21.95 % Favored : 75.36 % 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: 0.73 (0.20), residues: 1694 helix: 0.61 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : 0.53 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 71 HIS 0.013 0.002 HIS H 47 PHE 0.024 0.003 PHE J 122 TYR 0.035 0.003 TYR J 118 ARG 0.010 0.001 ARG C 39 *********************** 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 318 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 TYR cc_start: 0.3671 (m-80) cc_final: 0.2846 (t80) REVERT: G 117 GLU cc_start: 0.7337 (pt0) cc_final: 0.7046 (pt0) REVERT: E 40 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: E 66 MET cc_start: 0.7850 (mmm) cc_final: 0.7215 (mmp) REVERT: K 67 THR cc_start: 0.8266 (m) cc_final: 0.7903 (p) REVERT: K 83 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: K 87 SER cc_start: 0.8198 (t) cc_final: 0.7978 (p) REVERT: H 66 MET cc_start: 0.4656 (mmp) cc_final: 0.3152 (ptp) REVERT: J 93 MET cc_start: 0.5310 (mmm) cc_final: 0.4520 (mpp) REVERT: L 9 PHE cc_start: 0.4718 (m-10) cc_final: 0.4274 (m-80) outliers start: 41 outliers final: 9 residues processed: 300 average time/residue: 1.1870 time to fit residues: 391.0267 Evaluate side-chains 224 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 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 E residue 112 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain F residue 72 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.0980 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN A 104 HIS D 57 GLN ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN I 47 HIS J 47 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 1.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14166 Z= 0.212 Angle : 0.704 10.249 19399 Z= 0.345 Chirality : 0.042 0.377 2193 Planarity : 0.005 0.048 2457 Dihedral : 4.424 19.945 1862 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 25.36 % Favored : 73.59 % 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: 1.31 (0.21), residues: 1694 helix: 1.01 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : 0.83 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 71 HIS 0.006 0.001 HIS A 104 PHE 0.016 0.002 PHE A 24 TYR 0.018 0.001 TYR H 132 ARG 0.007 0.001 ARG I 39 *********************** 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 245 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7053 (pm20) cc_final: 0.6831 (pm20) REVERT: B 96 LYS cc_start: 0.7623 (mttp) cc_final: 0.7387 (mttp) REVERT: A 132 TYR cc_start: 0.3536 (m-80) cc_final: 0.2601 (t80) REVERT: C 124 VAL cc_start: 0.8610 (t) cc_final: 0.8409 (t) REVERT: D 26 SER cc_start: 0.7938 (m) cc_final: 0.7669 (p) REVERT: G 117 GLU cc_start: 0.7254 (pt0) cc_final: 0.6965 (pt0) REVERT: E 7 LYS cc_start: 0.8166 (tppt) cc_final: 0.7947 (mmtm) REVERT: I 39 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7355 (ttt180) REVERT: K 68 LEU cc_start: 0.6122 (tt) cc_final: 0.5628 (tt) REVERT: K 83 ASP cc_start: 0.7816 (t70) cc_final: 0.7310 (m-30) REVERT: K 87 SER cc_start: 0.8379 (t) cc_final: 0.8040 (p) REVERT: J 93 MET cc_start: 0.5453 (mmm) cc_final: 0.4771 (mpp) outliers start: 16 outliers final: 7 residues processed: 241 average time/residue: 1.2792 time to fit residues: 337.0713 Evaluate side-chains 214 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 THR Chi-restraints excluded: chain K residue 99 GLN Chi-restraints excluded: chain K residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 13 optimal weight: 0.0050 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** G 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 1.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14166 Z= 0.278 Angle : 0.760 9.890 19399 Z= 0.373 Chirality : 0.045 0.405 2193 Planarity : 0.006 0.048 2457 Dihedral : 4.450 19.257 1862 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.11 % Allowed : 26.28 % Favored : 72.61 % 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: 1.15 (0.20), residues: 1694 helix: 0.90 (0.14), residues: 1259 sheet: None (None), residues: 0 loop : 0.71 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 71 HIS 0.011 0.002 HIS F 51 PHE 0.020 0.002 PHE J 97 TYR 0.021 0.002 TYR F 38 ARG 0.008 0.001 ARG F 127 ********************** 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 262 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.4274 (m-80) cc_final: 0.3179 (t80) REVERT: C 14 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: C 124 VAL cc_start: 0.8687 (t) cc_final: 0.8440 (t) REVERT: G 67 THR cc_start: 0.8997 (m) cc_final: 0.8582 (p) REVERT: G 117 GLU cc_start: 0.7336 (pt0) cc_final: 0.7030 (pt0) REVERT: E 7 LYS cc_start: 0.8274 (tppt) cc_final: 0.8051 (mmtm) REVERT: K 65 LEU cc_start: 0.8008 (tm) cc_final: 0.7734 (mm) REVERT: K 83 ASP cc_start: 0.7812 (t70) cc_final: 0.7338 (m-30) REVERT: K 87 SER cc_start: 0.8433 (t) cc_final: 0.8206 (p) REVERT: J 93 MET cc_start: 0.5943 (mmm) cc_final: 0.5215 (mpp) REVERT: J 144 PRO cc_start: 0.7751 (Cg_exo) cc_final: 0.7494 (Cg_endo) REVERT: L 9 PHE cc_start: 0.4969 (m-10) cc_final: 0.4648 (m-80) outliers start: 17 outliers final: 8 residues processed: 257 average time/residue: 1.2813 time to fit residues: 359.6045 Evaluate side-chains 225 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 GLU 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 67 THR Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 27 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.0060 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 HIS ** L 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.156916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132327 restraints weight = 22408.391| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.80 r_work: 0.3648 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 1.5116 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= 0.192 Angle : 0.708 13.452 19399 Z= 0.344 Chirality : 0.042 0.331 2193 Planarity : 0.005 0.048 2457 Dihedral : 4.269 18.475 1862 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.92 % Allowed : 27.39 % Favored : 71.69 % 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: 1.37 (0.21), residues: 1694 helix: 1.08 (0.15), residues: 1252 sheet: None (None), residues: 0 loop : 0.77 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 71 HIS 0.006 0.001 HIS F 51 PHE 0.015 0.001 PHE A 24 TYR 0.016 0.001 TYR H 132 ARG 0.011 0.001 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5645.28 seconds wall clock time: 102 minutes 3.64 seconds (6123.64 seconds total)