Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 11:12:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6se6_10152/07_2023/6se6_10152.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6706 2.51 5 N 2263 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "V ARG 522": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 12068 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 812 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "V" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Time building chain proxies: 6.28, per 1000 atoms: 0.52 Number of scatterers: 12068 At special positions: 0 Unit cell: (78, 120.25, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2801 8.00 N 2263 7.00 C 6706 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: 6.44 Conformation dependent library (CDL) restraints added in 928.0 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 69.4% alpha, 2.3% beta 144 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.271A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.526A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.808A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.547A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.705A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.234A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.668A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.673A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.458A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.836A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.594A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.192A pdb=" N LYS E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.565A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.785A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.276A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.745A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.631A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 4.070A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.654A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.990A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.771A pdb=" N ASN H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.511A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.594A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.073A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.658A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.678A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 351 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 686 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1874 1.32 - 1.44: 4461 1.44 - 1.56: 5947 1.56 - 1.68: 580 1.68 - 1.79: 18 Bond restraints: 12880 Sorted by residual: bond pdb=" CB VAL C 27 " pdb=" CG2 VAL C 27 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.27e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.99e+00 bond pdb=" CB THR F 73 " pdb=" CG2 THR F 73 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" CB VAL G 27 " pdb=" CG2 VAL G 27 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.74e+00 ... (remaining 12875 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.79: 1211 104.79 - 112.10: 6990 112.10 - 119.41: 4302 119.41 - 126.72: 5310 126.72 - 134.03: 824 Bond angle restraints: 18637 Sorted by residual: angle pdb=" C THR A 79 " pdb=" N ARG A 80 " pdb=" CA ARG A 80 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C ARG A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta sigma weight residual 122.46 127.70 -5.24 1.41e+00 5.03e-01 1.38e+01 angle pdb=" CA TRP V 530 " pdb=" CB TRP V 530 " pdb=" CG TRP V 530 " ideal model delta sigma weight residual 113.60 120.65 -7.05 1.90e+00 2.77e-01 1.38e+01 angle pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sigma weight residual 120.20 125.57 -5.37 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C3' DC I -29 " pdb=" O3' DC I -29 " pdb=" P DT I -28 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 ... (remaining 18632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 5315 35.73 - 71.45: 1361 71.45 - 107.18: 18 107.18 - 142.90: 6 142.90 - 178.63: 2 Dihedral angle restraints: 6702 sinusoidal: 4484 harmonic: 2218 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.63 -178.63 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 75.72 144.28 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 94.35 125.65 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 6699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1290 0.047 - 0.093: 600 0.093 - 0.140: 167 0.140 - 0.187: 51 0.187 - 0.233: 6 Chirality restraints: 2114 Sorted by residual: chirality pdb=" CG LEU G 97 " pdb=" CB LEU G 97 " pdb=" CD1 LEU G 97 " pdb=" CD2 LEU G 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2111 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.054 2.00e-02 2.50e+03 2.34e-02 1.64e+01 pdb=" N9 DG I 26 " 0.056 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.043 2.00e-02 2.50e+03 1.98e-02 1.18e+01 pdb=" N9 DG I 28 " 0.049 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.016 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -26 " 0.044 2.00e-02 2.50e+03 2.06e-02 1.07e+01 pdb=" N1 DT I -26 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DT I -26 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT I -26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I -26 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O4 DT I -26 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DT I -26 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I -26 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I -26 " -0.008 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2460 2.78 - 3.31: 10073 3.31 - 3.84: 24303 3.84 - 4.37: 27108 4.37 - 4.90: 38480 Nonbonded interactions: 102424 Sorted by model distance: nonbonded pdb=" O2 DC I -4 " pdb=" N2 DG J 4 " model vdw 2.247 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.249 2.496 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.264 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.268 2.496 nonbonded pdb=" O2 DC I 5 " pdb=" N2 DG J -5 " model vdw 2.275 2.496 ... (remaining 102419 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 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 116) } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.130 Check model and map are aligned: 0.000 Set scattering table: 0.080 Process input model: 40.040 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.010 0.095 12880 Z= 0.593 Angle : 0.998 12.172 18637 Z= 0.571 Chirality : 0.059 0.233 2114 Planarity : 0.008 0.074 1347 Dihedral : 28.155 178.630 5272 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.00 % 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: -3.83 (0.22), residues: 753 helix: -2.55 (0.16), residues: 508 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.3698 time to fit residues: 111.7964 Evaluate side-chains 178 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 27 GLN B 93 GLN C 31 HIS C 73 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12880 Z= 0.229 Angle : 0.618 6.032 18637 Z= 0.367 Chirality : 0.035 0.177 2114 Planarity : 0.004 0.045 1347 Dihedral : 31.359 175.067 3763 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 2.51 % 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: -0.84 (0.27), residues: 753 helix: 0.09 (0.21), residues: 517 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 216 average time/residue: 0.2819 time to fit residues: 82.1752 Evaluate side-chains 198 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1098 time to fit residues: 3.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12880 Z= 0.236 Angle : 0.596 8.971 18637 Z= 0.352 Chirality : 0.034 0.156 2114 Planarity : 0.004 0.035 1347 Dihedral : 31.220 174.251 3763 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 2.19 % 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: 0.45 (0.29), residues: 753 helix: 1.21 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.76 (0.33), residues: 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 209 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 213 average time/residue: 0.3030 time to fit residues: 87.1601 Evaluate side-chains 201 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1439 time to fit residues: 3.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 31 HIS F 75 HIS ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12880 Z= 0.188 Angle : 0.571 5.970 18637 Z= 0.339 Chirality : 0.032 0.156 2114 Planarity : 0.003 0.038 1347 Dihedral : 31.108 172.692 3763 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 2.04 % 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: 1.03 (0.30), residues: 753 helix: 1.59 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 210 average time/residue: 0.2834 time to fit residues: 80.8318 Evaluate side-chains 192 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1048 time to fit residues: 2.0925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 12880 Z= 0.356 Angle : 0.644 8.240 18637 Z= 0.372 Chirality : 0.036 0.155 2114 Planarity : 0.004 0.031 1347 Dihedral : 31.292 168.787 3763 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 3.61 % 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: 0.93 (0.30), residues: 753 helix: 1.53 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.44 (0.35), residues: 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 192 average time/residue: 0.2790 time to fit residues: 73.0523 Evaluate side-chains 192 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1073 time to fit residues: 4.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12880 Z= 0.242 Angle : 0.600 6.971 18637 Z= 0.351 Chirality : 0.034 0.150 2114 Planarity : 0.003 0.034 1347 Dihedral : 31.220 167.795 3763 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 1.57 % 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: 1.17 (0.30), residues: 753 helix: 1.69 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.33 (0.36), residues: 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 194 average time/residue: 0.2716 time to fit residues: 72.3568 Evaluate side-chains 185 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1133 time to fit residues: 2.3555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12880 Z= 0.220 Angle : 0.587 7.688 18637 Z= 0.346 Chirality : 0.033 0.151 2114 Planarity : 0.004 0.036 1347 Dihedral : 31.112 164.893 3763 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.10 % 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: 1.30 (0.30), residues: 753 helix: 1.78 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.25 (0.36), residues: 236 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 191 average time/residue: 0.2561 time to fit residues: 68.2769 Evaluate side-chains 186 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1054 time to fit residues: 2.3124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 12880 Z= 0.351 Angle : 0.650 6.409 18637 Z= 0.378 Chirality : 0.036 0.174 2114 Planarity : 0.004 0.030 1347 Dihedral : 31.222 159.647 3763 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.88 % 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: 0.96 (0.30), residues: 753 helix: 1.55 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 180 average time/residue: 0.2663 time to fit residues: 66.4455 Evaluate side-chains 179 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1155 time to fit residues: 3.2699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 12880 Z= 0.339 Angle : 0.657 8.521 18637 Z= 0.381 Chirality : 0.036 0.173 2114 Planarity : 0.004 0.030 1347 Dihedral : 31.231 161.758 3763 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.47 % 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: 0.82 (0.30), residues: 753 helix: 1.42 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 178 average time/residue: 0.2764 time to fit residues: 68.9252 Evaluate side-chains 174 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1114 time to fit residues: 1.7315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12880 Z= 0.256 Angle : 0.629 8.537 18637 Z= 0.367 Chirality : 0.034 0.162 2114 Planarity : 0.004 0.033 1347 Dihedral : 31.137 165.657 3763 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 0.94 % 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: 0.97 (0.30), residues: 753 helix: 1.55 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.43 (0.35), residues: 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 178 average time/residue: 0.2655 time to fit residues: 66.0140 Evaluate side-chains 178 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1047 time to fit residues: 2.0876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.086578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060284 restraints weight = 40618.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.062218 restraints weight = 20261.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063444 restraints weight = 13671.250| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12880 Z= 0.214 Angle : 0.622 10.397 18637 Z= 0.361 Chirality : 0.033 0.163 2114 Planarity : 0.004 0.035 1347 Dihedral : 31.041 169.765 3763 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.31 % 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: 1.17 (0.30), residues: 753 helix: 1.72 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 237 =============================================================================== Job complete usr+sys time: 2092.66 seconds wall clock time: 38 minutes 56.84 seconds (2336.84 seconds total)