Starting phenix.real_space_refine (version: dev) on Sat Feb 18 23:42:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4g_30077/02_2023/6m4g_30077.pdb" } resolution = 2.8 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= -0.002 sd= 1.046 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 Process input model Symmetric amino acids flipped Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9010 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1924 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1888 Classifications: {'DNA': 93} Link IDs: {'rna3p': 92} Chain: "A" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "E" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 599 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "H" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 705 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Time building chain proxies: 5.44, per 1000 atoms: 0.60 Number of scatterers: 9010 At special positions: 0 Unit cell: (80.08, 115.44, 115.44, 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 16 16.00 P 186 15.00 O 2064 8.00 N 1657 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 914.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 75.9% alpha, 2.1% beta 66 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 3.42 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.584A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.532A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 84 removed outlier: 3.608A pdb=" N GLY D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.690A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.583A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.628A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.634A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.648A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.703A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 84 removed outlier: 3.607A pdb=" N GLY H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.689A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 removed outlier: 4.028A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 78 removed outlier: 3.866A pdb=" N GLU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 30 through 42 removed outlier: 3.538A pdb=" N VAL G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 78 removed outlier: 3.865A pdb=" N GLU G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.624A pdb=" N HIS G 92 " --> pdb=" O ASP G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.336A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.122A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.674A pdb=" N THR F 96 " --> pdb=" O THR C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 325 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 169 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1683 1.33 - 1.45: 3039 1.45 - 1.57: 4417 1.57 - 1.68: 372 1.68 - 1.80: 28 Bond restraints: 9539 Sorted by residual: bond pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.38e+00 bond pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" C4' DC J 64 " pdb=" O4' DC J 64 " ideal model delta sigma weight residual 1.450 1.415 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" C3' DG I 38 " pdb=" C2' DG I 38 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C4' DC I 85 " pdb=" O4' DC I 85 " ideal model delta sigma weight residual 1.450 1.417 0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 9534 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.66: 723 104.66 - 111.70: 4883 111.70 - 118.74: 2957 118.74 - 125.79: 4518 125.79 - 132.83: 604 Bond angle restraints: 13685 Sorted by residual: angle pdb=" C2' DG I 53 " pdb=" C1' DG I 53 " pdb=" N9 DG I 53 " ideal model delta sigma weight residual 113.50 120.84 -7.34 1.50e+00 4.44e-01 2.39e+01 angle pdb=" C2' DG I 32 " pdb=" C1' DG I 32 " pdb=" N9 DG I 32 " ideal model delta sigma weight residual 113.50 120.34 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C2' DT I 57 " pdb=" C1' DT I 57 " pdb=" N1 DT I 57 " ideal model delta sigma weight residual 113.50 120.07 -6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" CB GLU F 53 " pdb=" CG GLU F 53 " pdb=" CD GLU F 53 " ideal model delta sigma weight residual 112.60 119.76 -7.16 1.70e+00 3.46e-01 1.77e+01 angle pdb=" CB GLU B 53 " pdb=" CG GLU B 53 " pdb=" CD GLU B 53 " ideal model delta sigma weight residual 112.60 119.74 -7.14 1.70e+00 3.46e-01 1.76e+01 ... (remaining 13680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 4217 33.38 - 66.75: 853 66.75 - 100.13: 17 100.13 - 133.51: 1 133.51 - 166.88: 6 Dihedral angle restraints: 5094 sinusoidal: 3176 harmonic: 1918 Sorted by residual: dihedral pdb=" C4' DT J 32 " pdb=" C3' DT J 32 " pdb=" O3' DT J 32 " pdb=" P DG J 33 " ideal model delta sinusoidal sigma weight residual 220.00 53.12 166.88 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " pdb=" P DA I 90 " ideal model delta sinusoidal sigma weight residual 220.00 65.43 154.57 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS C 92 " pdb=" C HIS C 92 " pdb=" N ASN C 93 " pdb=" CA ASN C 93 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1464 0.101 - 0.201: 117 0.201 - 0.302: 2 0.302 - 0.402: 1 0.402 - 0.503: 2 Chirality restraints: 1586 Sorted by residual: chirality pdb=" C1' DG I 53 " pdb=" O4' DG I 53 " pdb=" C2' DG I 53 " pdb=" N9 DG I 53 " both_signs ideal model delta sigma weight residual False 2.42 1.92 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" C1' DT I 57 " pdb=" O4' DT I 57 " pdb=" C2' DT I 57 " pdb=" N1 DT I 57 " both_signs ideal model delta sigma weight residual False 2.47 1.99 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1' DC J 28 " pdb=" O4' DC J 28 " pdb=" C2' DC J 28 " pdb=" N1 DC J 28 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1583 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 117 " 0.021 2.00e-02 2.50e+03 4.80e-02 6.33e+01 pdb=" N9 DA I 117 " -0.122 2.00e-02 2.50e+03 pdb=" C8 DA I 117 " 0.095 2.00e-02 2.50e+03 pdb=" N7 DA I 117 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DA I 117 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 117 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 117 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 117 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 117 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DA I 117 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DA I 117 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 116 " 0.038 2.00e-02 2.50e+03 3.97e-02 3.55e+01 pdb=" N1 DC J 116 " -0.095 2.00e-02 2.50e+03 pdb=" C2 DC J 116 " 0.057 2.00e-02 2.50e+03 pdb=" O2 DC J 116 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC J 116 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 116 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 116 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 116 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DC J 116 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 32 " -0.063 2.00e-02 2.50e+03 2.80e-02 2.36e+01 pdb=" N9 DG I 32 " 0.070 2.00e-02 2.50e+03 pdb=" C8 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 32 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 32 " -0.016 2.00e-02 2.50e+03 pdb=" N1 DG I 32 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG I 32 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 32 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DG I 32 " 0.006 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 831 2.72 - 3.26: 7789 3.26 - 3.81: 16217 3.81 - 4.35: 21301 4.35 - 4.90: 30325 Nonbonded interactions: 76463 Sorted by model distance: nonbonded pdb=" OE1 GLU D 76 " pdb=" NH2 ARG D 79 " model vdw 2.169 2.520 nonbonded pdb=" OE1 GLU H 76 " pdb=" NH2 ARG H 79 " model vdw 2.170 2.520 nonbonded pdb=" O HIS F 75 " pdb=" NH1 ARG H 92 " model vdw 2.248 2.520 nonbonded pdb=" N2 DG I 32 " pdb=" O2 DC J 116 " model vdw 2.254 2.520 nonbonded pdb=" OP2 DA J 91 " pdb=" NH2 ARG E 69 " model vdw 2.267 2.520 ... (remaining 76458 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' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 186 5.49 5 S 16 5.16 5 C 5087 2.51 5 N 1657 2.21 5 O 2064 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.830 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: 3.900 Check model and map are aligned: 0.150 Process input model: 29.640 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:17.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.006 0.055 9539 Z= 0.362 Angle : 0.931 7.338 13685 Z= 0.578 Chirality : 0.058 0.503 1586 Planarity : 0.010 0.062 1080 Dihedral : 25.709 166.884 3850 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.14 % 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: -6.14 (0.18), residues: 640 helix: -4.12 (0.10), residues: 458 sheet: None (None), residues: 0 loop : -3.19 (0.32), residues: 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 0.767 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 168 average time/residue: 1.3080 time to fit residues: 233.1379 Evaluate side-chains 134 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 84 ASN D 109 HIS E 68 GLN H 84 ASN H 109 HIS C 33 GLN C 72 ASN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 GLN G 72 ASN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9539 Z= 0.197 Angle : 0.614 5.380 13685 Z= 0.358 Chirality : 0.037 0.152 1586 Planarity : 0.005 0.048 1080 Dihedral : 31.333 171.264 2590 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 3.38 % 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: -2.36 (0.28), residues: 640 helix: -1.13 (0.21), residues: 482 sheet: None (None), residues: 0 loop : -2.47 (0.38), residues: 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.776 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 136 average time/residue: 1.0990 time to fit residues: 160.1996 Evaluate side-chains 133 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 8 average time/residue: 0.2138 time to fit residues: 3.1843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 93 GLN C 33 GLN G 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 9539 Z= 0.260 Angle : 0.630 5.506 13685 Z= 0.364 Chirality : 0.039 0.169 1586 Planarity : 0.005 0.045 1080 Dihedral : 31.203 164.637 2590 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 4.45 % 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: -0.51 (0.31), residues: 640 helix: 0.26 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.962 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 140 average time/residue: 1.2885 time to fit residues: 191.6925 Evaluate side-chains 131 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.3363 time to fit residues: 3.3034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9539 Z= 0.192 Angle : 0.580 6.119 13685 Z= 0.338 Chirality : 0.036 0.155 1586 Planarity : 0.004 0.044 1080 Dihedral : 31.278 168.678 2590 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.32), residues: 640 helix: 0.88 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.887 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 129 average time/residue: 1.4482 time to fit residues: 197.8045 Evaluate side-chains 131 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.1645 time to fit residues: 2.4773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 84 ASN E 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 9539 Z= 0.332 Angle : 0.648 5.761 13685 Z= 0.372 Chirality : 0.041 0.180 1586 Planarity : 0.005 0.047 1080 Dihedral : 31.580 165.859 2590 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 4.45 % 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: 0.50 (0.32), residues: 640 helix: 0.97 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.86 (0.41), residues: 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.742 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 146 average time/residue: 1.3315 time to fit residues: 206.1405 Evaluate side-chains 146 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.1087 time to fit residues: 2.0176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** 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: 0.7783 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9539 Z= 0.219 Angle : 0.608 6.207 13685 Z= 0.355 Chirality : 0.038 0.188 1586 Planarity : 0.005 0.041 1080 Dihedral : 31.580 166.707 2590 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 3.56 % 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: 0.78 (0.32), residues: 640 helix: 1.18 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.78 (0.41), residues: 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.632 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 1.2977 time to fit residues: 202.5418 Evaluate side-chains 145 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 4 residues processed: 7 average time/residue: 0.1684 time to fit residues: 2.7810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 9539 Z= 0.211 Angle : 0.604 6.596 13685 Z= 0.350 Chirality : 0.037 0.196 1586 Planarity : 0.006 0.127 1080 Dihedral : 31.555 167.135 2590 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer Outliers : 2.49 % 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 (0.32), residues: 640 helix: 1.33 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.79 (0.41), residues: 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 0.709 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 141 average time/residue: 1.2687 time to fit residues: 189.9972 Evaluate side-chains 142 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.1317 time to fit residues: 1.8700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.0270 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 67 optimal weight: 8.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9539 Z= 0.232 Angle : 0.592 8.028 13685 Z= 0.343 Chirality : 0.037 0.167 1586 Planarity : 0.004 0.041 1080 Dihedral : 31.444 167.562 2590 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 1.60 % 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 (0.32), residues: 640 helix: 1.57 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.83 (0.39), residues: 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 138 average time/residue: 1.3203 time to fit residues: 193.1213 Evaluate side-chains 141 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4795 time to fit residues: 3.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 47 optimal weight: 0.0030 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9539 Z= 0.195 Angle : 0.589 7.856 13685 Z= 0.341 Chirality : 0.036 0.181 1586 Planarity : 0.005 0.082 1080 Dihedral : 31.454 167.741 2590 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.07 % 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: 1.27 (0.32), residues: 640 helix: 1.65 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 136 average time/residue: 1.3201 time to fit residues: 190.9479 Evaluate side-chains 136 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.2515 time to fit residues: 1.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 9539 Z= 0.301 Angle : 0.632 7.867 13685 Z= 0.361 Chirality : 0.040 0.195 1586 Planarity : 0.005 0.053 1080 Dihedral : 31.594 167.519 2590 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.89 % 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 (0.32), residues: 640 helix: 1.48 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.80 (0.41), residues: 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.684 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 139 average time/residue: 1.2929 time to fit residues: 190.7615 Evaluate side-chains 141 residues out of total 562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0778 time to fit residues: 1.1970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.0770 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.142918 restraints weight = 10927.782| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.03 r_work: 0.3539 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 9539 Z= 0.209 Angle : 0.616 7.697 13685 Z= 0.354 Chirality : 0.037 0.191 1586 Planarity : 0.005 0.040 1080 Dihedral : 31.601 167.673 2590 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 1.07 % 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: 1.26 (0.32), residues: 640 helix: 1.55 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 142 =============================================================================== Job complete usr+sys time: 3348.28 seconds wall clock time: 60 minutes 24.14 seconds (3624.14 seconds total)