Starting phenix.real_space_refine on Wed Sep 25 14:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b6d_12052/09_2024/7b6d_12052_neut.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 6713 2.51 5 N 1749 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10470 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Time building chain proxies: 6.51, per 1000 atoms: 0.62 Number of scatterers: 10470 At special positions: 0 Unit cell: (167.232, 152.256, 79.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1958 8.00 N 1749 7.00 C 6713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 43.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.567A pdb=" N GLY A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 63 removed outlier: 4.204A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 Processing helix chain 'A' and resid 126 through 140 removed outlier: 4.521A pdb=" N ALA A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 27 through 42 removed outlier: 4.352A pdb=" N GLU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 107 through 114 removed outlier: 3.814A pdb=" N LYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.635A pdb=" N ALA D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.810A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 210 Processing helix chain 'E' and resid 26 through 55 removed outlier: 3.634A pdb=" N ASP E 32 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 122 through 136 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 81 removed outlier: 3.573A pdb=" N LEU F 56 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.898A pdb=" N TRP F 100 " --> pdb=" O LYS F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.285A pdb=" N PHE F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 160 removed outlier: 3.691A pdb=" N PHE F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'G' and resid 14 through 33 Processing helix chain 'G' and resid 35 through 59 removed outlier: 3.703A pdb=" N VAL G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU G 56 " --> pdb=" O MET G 52 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 85 removed outlier: 3.579A pdb=" N PHE G 81 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.539A pdb=" N THR G 121 " --> pdb=" O PRO G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 140 removed outlier: 3.940A pdb=" N SER G 130 " --> pdb=" O SER G 126 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG G 134 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 48 Processing helix chain 'H' and resid 92 through 111 Processing helix chain 'H' and resid 123 through 138 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.223A pdb=" N PHE A 101 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 80 removed outlier: 4.172A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.129A pdb=" N LEU C 62 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 154 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 5 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 Processing sheet with id=AA5, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.500A pdb=" N ASP D 41 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 48 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.616A pdb=" N VAL D 66 " --> pdb=" O MET D 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 15 through 21 removed outlier: 4.233A pdb=" N TYR E 17 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR E 4 " --> pdb=" O PHE E 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.053A pdb=" N GLU G 160 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.740A pdb=" N LEU H 15 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA H 2 " --> pdb=" O ASP H 84 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP H 84 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS H 4 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL H 82 " --> pdb=" O CYS H 4 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL H 81 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS H 67 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS H 66 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3391 1.34 - 1.46: 2413 1.46 - 1.58: 4798 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 10683 Sorted by residual: bond pdb=" N GLY H 48 " pdb=" CA GLY H 48 " ideal model delta sigma weight residual 1.449 1.504 -0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" C GLY H 48 " pdb=" O GLY H 48 " ideal model delta sigma weight residual 1.235 1.281 -0.046 1.35e-02 5.49e+03 1.16e+01 bond pdb=" C TYR H 30 " pdb=" O TYR H 30 " ideal model delta sigma weight residual 1.235 1.275 -0.039 1.26e-02 6.30e+03 9.74e+00 bond pdb=" N VAL H 39 " pdb=" CA VAL H 39 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00 bond pdb=" C CYS H 43 " pdb=" O CYS H 43 " ideal model delta sigma weight residual 1.237 1.269 -0.033 1.17e-02 7.31e+03 7.78e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 14038 2.28 - 4.56: 369 4.56 - 6.84: 37 6.84 - 9.11: 5 9.11 - 11.39: 1 Bond angle restraints: 14450 Sorted by residual: angle pdb=" CA LYS H 47 " pdb=" C LYS H 47 " pdb=" O LYS H 47 " ideal model delta sigma weight residual 120.42 115.36 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" C GLU F 109 " pdb=" N LYS F 110 " pdb=" CA LYS F 110 " ideal model delta sigma weight residual 122.37 114.56 7.81 1.72e+00 3.38e-01 2.06e+01 angle pdb=" N LYS H 47 " pdb=" CA LYS H 47 " pdb=" C LYS H 47 " ideal model delta sigma weight residual 111.36 116.29 -4.93 1.09e+00 8.42e-01 2.05e+01 angle pdb=" CA PRO C 138 " pdb=" C PRO C 138 " pdb=" N ILE C 139 " ideal model delta sigma weight residual 115.95 121.01 -5.06 1.12e+00 7.97e-01 2.04e+01 angle pdb=" C PHE G 165 " pdb=" N VAL G 166 " pdb=" CA VAL G 166 " ideal model delta sigma weight residual 123.08 118.78 4.30 1.01e+00 9.80e-01 1.81e+01 ... (remaining 14445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5792 17.84 - 35.68: 553 35.68 - 53.52: 79 53.52 - 71.36: 16 71.36 - 89.20: 11 Dihedral angle restraints: 6451 sinusoidal: 2653 harmonic: 3798 Sorted by residual: dihedral pdb=" CA ASN D 216 " pdb=" C ASN D 216 " pdb=" N ILE D 217 " pdb=" CA ILE D 217 " ideal model delta harmonic sigma weight residual -180.00 -122.18 -57.82 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA PRO D 35 " pdb=" C PRO D 35 " pdb=" N LEU D 36 " pdb=" CA LEU D 36 " ideal model delta harmonic sigma weight residual 180.00 -142.52 -37.48 0 5.00e+00 4.00e-02 5.62e+01 dihedral pdb=" CA ASP C 87 " pdb=" C ASP C 87 " pdb=" N THR C 88 " pdb=" CA THR C 88 " ideal model delta harmonic sigma weight residual -180.00 -151.94 -28.06 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 6448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1367 0.068 - 0.137: 231 0.137 - 0.205: 27 0.205 - 0.274: 4 0.274 - 0.342: 2 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA LYS H 47 " pdb=" N LYS H 47 " pdb=" C LYS H 47 " pdb=" CB LYS H 47 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE F 123 " pdb=" CA ILE F 123 " pdb=" CG1 ILE F 123 " pdb=" CG2 ILE F 123 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE F 72 " pdb=" CA ILE F 72 " pdb=" CG1 ILE F 72 " pdb=" CG2 ILE F 72 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1628 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 48 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLY H 48 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY H 48 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA H 49 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 116 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 117 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " 0.051 5.00e-02 4.00e+02 7.80e-02 9.75e+00 pdb=" N PRO A 118 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " 0.043 5.00e-02 4.00e+02 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 216 2.62 - 3.19: 10941 3.19 - 3.76: 18086 3.76 - 4.33: 25073 4.33 - 4.90: 36828 Nonbonded interactions: 91144 Sorted by model distance: nonbonded pdb=" OH TYR E 102 " pdb=" OD1 ASP F 73 " model vdw 2.049 3.040 nonbonded pdb=" OG SER G 102 " pdb=" NH1 ARG G 162 " model vdw 2.085 3.120 nonbonded pdb=" O GLU A 69 " pdb=" OG1 THR A 73 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASP A 38 " pdb=" NZ LYS A 41 " model vdw 2.145 3.120 nonbonded pdb=" O TYR F 45 " pdb=" OG SER F 48 " model vdw 2.161 3.040 ... (remaining 91139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'G' and resid 10 through 174) } 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: 2.600 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 : 0.005 0.088 10683 Z= 0.295 Angle : 0.875 11.392 14450 Z= 0.521 Chirality : 0.053 0.342 1631 Planarity : 0.006 0.082 1849 Dihedral : 14.401 89.202 3985 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.20 % Favored : 89.72 % Rotamer: Outliers : 0.43 % Allowed : 0.69 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.46 (0.22), residues: 1274 helix: -0.82 (0.22), residues: 505 sheet: -1.36 (0.35), residues: 208 loop : -2.48 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP F 100 HIS 0.008 0.001 HIS B 11 PHE 0.032 0.003 PHE C 82 TYR 0.021 0.002 TYR F 75 ARG 0.011 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8503 (mmp) cc_final: 0.8065 (mmm) REVERT: A 50 MET cc_start: 0.8292 (tmm) cc_final: 0.7942 (tmm) REVERT: A 70 MET cc_start: 0.8530 (tpp) cc_final: 0.8264 (tpp) REVERT: B 68 MET cc_start: 0.8528 (mmm) cc_final: 0.8277 (mmm) REVERT: C 56 ASP cc_start: 0.7077 (m-30) cc_final: 0.6637 (t70) REVERT: E 18 GLU cc_start: 0.8481 (pp20) cc_final: 0.8147 (pp20) REVERT: E 42 HIS cc_start: 0.8747 (m-70) cc_final: 0.8439 (t70) REVERT: E 83 ILE cc_start: 0.9205 (mm) cc_final: 0.8792 (tp) REVERT: E 110 MET cc_start: 0.8913 (mpp) cc_final: 0.8580 (mpp) REVERT: E 130 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8449 (tm-30) REVERT: F 124 ILE cc_start: 0.7148 (tt) cc_final: 0.6915 (tp) REVERT: G 148 PHE cc_start: 0.8853 (m-80) cc_final: 0.8511 (m-80) REVERT: H 1 MET cc_start: 0.0673 (mmm) cc_final: 0.0281 (tpt) REVERT: H 16 TYR cc_start: 0.8345 (p90) cc_final: 0.7859 (p90) REVERT: H 102 LEU cc_start: 0.9569 (tp) cc_final: 0.9341 (tt) REVERT: H 122 THR cc_start: 0.6134 (p) cc_final: 0.5795 (t) outliers start: 5 outliers final: 0 residues processed: 135 average time/residue: 0.2075 time to fit residues: 40.6081 Evaluate side-chains 90 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10683 Z= 0.220 Angle : 0.721 8.773 14450 Z= 0.387 Chirality : 0.047 0.203 1631 Planarity : 0.005 0.052 1849 Dihedral : 7.338 71.650 1405 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.34 % Allowed : 7.63 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.09 (0.23), residues: 1274 helix: -0.40 (0.22), residues: 519 sheet: -1.47 (0.34), residues: 216 loop : -2.29 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 100 HIS 0.009 0.001 HIS E 51 PHE 0.028 0.002 PHE B 35 TYR 0.027 0.002 TYR B 17 ARG 0.008 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8291 (mmp) cc_final: 0.8059 (mmm) REVERT: A 70 MET cc_start: 0.8518 (tpp) cc_final: 0.8106 (tpp) REVERT: C 41 MET cc_start: 0.8696 (mmm) cc_final: 0.8393 (mtp) REVERT: C 56 ASP cc_start: 0.7429 (m-30) cc_final: 0.6842 (t70) REVERT: E 18 GLU cc_start: 0.8406 (pp20) cc_final: 0.8166 (pp20) REVERT: E 42 HIS cc_start: 0.8654 (m90) cc_final: 0.8373 (m170) REVERT: E 81 ARG cc_start: 0.7990 (mpt-90) cc_final: 0.7784 (mpt-90) REVERT: E 83 ILE cc_start: 0.9296 (mm) cc_final: 0.8978 (tp) REVERT: E 97 PHE cc_start: 0.8367 (t80) cc_final: 0.8090 (t80) REVERT: E 134 ARG cc_start: 0.7570 (mpp-170) cc_final: 0.7305 (mmp80) REVERT: E 138 LEU cc_start: 0.7335 (tp) cc_final: 0.6320 (tp) REVERT: F 147 ASN cc_start: 0.8177 (t0) cc_final: 0.7870 (t0) REVERT: F 177 MET cc_start: 0.8152 (tmm) cc_final: 0.7689 (tmm) REVERT: G 43 LEU cc_start: 0.9170 (tt) cc_final: 0.8864 (pp) REVERT: G 148 PHE cc_start: 0.8802 (m-80) cc_final: 0.8401 (m-80) REVERT: H 16 TYR cc_start: 0.8255 (p90) cc_final: 0.7803 (p90) REVERT: H 134 MET cc_start: 0.6364 (tpt) cc_final: 0.5568 (tpp) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.2278 time to fit residues: 42.1193 Evaluate side-chains 88 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN F 32 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10683 Z= 0.196 Angle : 0.695 9.143 14450 Z= 0.373 Chirality : 0.046 0.247 1631 Planarity : 0.005 0.041 1849 Dihedral : 6.967 71.853 1405 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.26 % Allowed : 4.03 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.83 (0.23), residues: 1274 helix: -0.11 (0.22), residues: 517 sheet: -1.31 (0.34), residues: 212 loop : -2.24 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 147 HIS 0.012 0.001 HIS B 11 PHE 0.026 0.002 PHE B 35 TYR 0.027 0.002 TYR E 102 ARG 0.008 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8535 (tpp) cc_final: 0.8078 (tpp) REVERT: B 115 PHE cc_start: 0.7697 (t80) cc_final: 0.7271 (t80) REVERT: C 41 MET cc_start: 0.8673 (mmm) cc_final: 0.8366 (mtp) REVERT: C 56 ASP cc_start: 0.7329 (m-30) cc_final: 0.6792 (t70) REVERT: D 69 MET cc_start: 0.7740 (pmm) cc_final: 0.7400 (pmm) REVERT: E 1 MET cc_start: 0.5643 (ppp) cc_final: 0.5375 (ppp) REVERT: E 18 GLU cc_start: 0.8401 (pp20) cc_final: 0.8176 (pp20) REVERT: E 42 HIS cc_start: 0.8646 (m90) cc_final: 0.8252 (m-70) REVERT: E 83 ILE cc_start: 0.9245 (mm) cc_final: 0.8918 (tp) REVERT: F 147 ASN cc_start: 0.7930 (t0) cc_final: 0.7727 (t0) REVERT: F 177 MET cc_start: 0.8072 (tmm) cc_final: 0.7819 (tmm) REVERT: F 194 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7265 (mmpt) REVERT: G 105 PHE cc_start: 0.7631 (m-80) cc_final: 0.7253 (m-80) REVERT: G 148 PHE cc_start: 0.8763 (m-80) cc_final: 0.8343 (m-10) REVERT: H 16 TYR cc_start: 0.8203 (p90) cc_final: 0.7755 (p90) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 0.2184 time to fit residues: 40.2746 Evaluate side-chains 84 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10683 Z= 0.196 Angle : 0.662 6.257 14450 Z= 0.358 Chirality : 0.045 0.194 1631 Planarity : 0.005 0.064 1849 Dihedral : 6.704 70.423 1405 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.26 % Allowed : 5.66 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.73 (0.23), residues: 1274 helix: -0.01 (0.22), residues: 519 sheet: -1.23 (0.35), residues: 208 loop : -2.22 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 147 HIS 0.010 0.001 HIS B 11 PHE 0.023 0.002 PHE B 35 TYR 0.032 0.002 TYR G 48 ARG 0.005 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8678 (mmm) cc_final: 0.8289 (mmm) REVERT: A 70 MET cc_start: 0.8368 (tpp) cc_final: 0.7879 (tpp) REVERT: C 41 MET cc_start: 0.8664 (mmm) cc_final: 0.8347 (mtp) REVERT: E 18 GLU cc_start: 0.8376 (pp20) cc_final: 0.8154 (pp20) REVERT: E 42 HIS cc_start: 0.8558 (m90) cc_final: 0.8154 (m-70) REVERT: E 83 ILE cc_start: 0.9247 (mm) cc_final: 0.8932 (tp) REVERT: E 130 GLU cc_start: 0.8928 (tp30) cc_final: 0.8513 (mt-10) REVERT: E 134 ARG cc_start: 0.7765 (mpp-170) cc_final: 0.7051 (mmp80) REVERT: E 138 LEU cc_start: 0.7478 (tp) cc_final: 0.7064 (tp) REVERT: F 147 ASN cc_start: 0.7965 (t0) cc_final: 0.7760 (t0) REVERT: G 50 MET cc_start: 0.8747 (mtp) cc_final: 0.8503 (tpp) REVERT: G 52 MET cc_start: 0.8420 (mtm) cc_final: 0.7468 (mmm) REVERT: G 105 PHE cc_start: 0.7626 (m-80) cc_final: 0.7295 (m-80) REVERT: G 139 MET cc_start: 0.7328 (tpp) cc_final: 0.6992 (tpp) REVERT: G 148 PHE cc_start: 0.8759 (m-80) cc_final: 0.8146 (m-80) REVERT: H 16 TYR cc_start: 0.8208 (p90) cc_final: 0.7768 (p90) outliers start: 3 outliers final: 0 residues processed: 123 average time/residue: 0.2272 time to fit residues: 40.3522 Evaluate side-chains 86 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10683 Z= 0.199 Angle : 0.676 8.191 14450 Z= 0.360 Chirality : 0.046 0.251 1631 Planarity : 0.004 0.048 1849 Dihedral : 6.582 72.826 1405 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.61 (0.23), residues: 1274 helix: 0.09 (0.23), residues: 517 sheet: -1.14 (0.35), residues: 209 loop : -2.16 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 100 HIS 0.007 0.001 HIS B 11 PHE 0.021 0.002 PHE B 115 TYR 0.027 0.002 TYR B 32 ARG 0.006 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8774 (mmm) cc_final: 0.8349 (mmm) REVERT: A 70 MET cc_start: 0.8298 (tpp) cc_final: 0.7805 (tpp) REVERT: C 41 MET cc_start: 0.8663 (mmm) cc_final: 0.8385 (mtp) REVERT: D 97 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8285 (tptp) REVERT: E 1 MET cc_start: 0.5714 (ppp) cc_final: 0.5490 (ppp) REVERT: E 18 GLU cc_start: 0.8391 (pp20) cc_final: 0.8176 (pp20) REVERT: E 83 ILE cc_start: 0.9238 (mm) cc_final: 0.8937 (tp) REVERT: E 130 GLU cc_start: 0.8817 (tp30) cc_final: 0.8538 (mt-10) REVERT: E 134 ARG cc_start: 0.7901 (mpp-170) cc_final: 0.7159 (mmp80) REVERT: E 138 LEU cc_start: 0.7547 (tp) cc_final: 0.6997 (tp) REVERT: F 113 HIS cc_start: 0.8546 (p-80) cc_final: 0.8282 (p-80) REVERT: F 147 ASN cc_start: 0.8242 (t0) cc_final: 0.7973 (t0) REVERT: G 43 LEU cc_start: 0.9208 (tt) cc_final: 0.8841 (pp) REVERT: G 50 MET cc_start: 0.8763 (mtp) cc_final: 0.8543 (ttm) REVERT: G 105 PHE cc_start: 0.7670 (m-80) cc_final: 0.7213 (m-80) REVERT: G 129 LEU cc_start: 0.8697 (mm) cc_final: 0.8456 (mp) REVERT: G 139 MET cc_start: 0.7385 (tpp) cc_final: 0.7123 (tpp) REVERT: G 148 PHE cc_start: 0.8801 (m-80) cc_final: 0.8499 (m-80) REVERT: H 16 TYR cc_start: 0.8254 (p90) cc_final: 0.7782 (p90) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2518 time to fit residues: 42.2338 Evaluate side-chains 80 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10683 Z= 0.189 Angle : 0.657 7.728 14450 Z= 0.349 Chirality : 0.045 0.211 1631 Planarity : 0.004 0.043 1849 Dihedral : 6.417 72.051 1405 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.51 (0.23), residues: 1274 helix: 0.14 (0.22), residues: 524 sheet: -1.01 (0.35), residues: 207 loop : -2.13 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 94 HIS 0.007 0.001 HIS B 11 PHE 0.013 0.002 PHE G 105 TYR 0.028 0.002 TYR G 48 ARG 0.007 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8779 (mmm) cc_final: 0.8327 (mmm) REVERT: A 70 MET cc_start: 0.8301 (tpp) cc_final: 0.7791 (tpp) REVERT: C 41 MET cc_start: 0.8663 (mmm) cc_final: 0.8394 (mtp) REVERT: C 56 ASP cc_start: 0.7424 (m-30) cc_final: 0.6939 (t70) REVERT: E 1 MET cc_start: 0.5726 (ppp) cc_final: 0.5480 (ppp) REVERT: E 18 GLU cc_start: 0.8375 (pp20) cc_final: 0.8161 (pp20) REVERT: E 83 ILE cc_start: 0.9204 (mm) cc_final: 0.8896 (tp) REVERT: E 134 ARG cc_start: 0.8101 (mpp-170) cc_final: 0.7873 (mmp80) REVERT: E 138 LEU cc_start: 0.7476 (tp) cc_final: 0.7204 (tp) REVERT: F 113 HIS cc_start: 0.8528 (p-80) cc_final: 0.8268 (p-80) REVERT: F 163 PRO cc_start: 0.7865 (Cg_exo) cc_final: 0.7641 (Cg_endo) REVERT: G 50 MET cc_start: 0.8811 (mtp) cc_final: 0.8605 (ttm) REVERT: G 105 PHE cc_start: 0.7714 (m-80) cc_final: 0.7333 (m-80) REVERT: G 129 LEU cc_start: 0.8713 (mm) cc_final: 0.8454 (mp) REVERT: G 139 MET cc_start: 0.7479 (tpp) cc_final: 0.7272 (tpp) REVERT: G 148 PHE cc_start: 0.8773 (m-80) cc_final: 0.8531 (m-80) REVERT: H 16 TYR cc_start: 0.8255 (p90) cc_final: 0.7796 (p90) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2327 time to fit residues: 43.2439 Evaluate side-chains 86 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.0770 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10683 Z= 0.193 Angle : 0.667 7.232 14450 Z= 0.354 Chirality : 0.046 0.244 1631 Planarity : 0.004 0.040 1849 Dihedral : 6.337 72.953 1405 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.44 (0.23), residues: 1274 helix: 0.23 (0.22), residues: 519 sheet: -1.06 (0.34), residues: 211 loop : -2.08 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 100 HIS 0.009 0.001 HIS B 146 PHE 0.014 0.002 PHE B 35 TYR 0.027 0.002 TYR G 48 ARG 0.004 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8743 (mmm) cc_final: 0.8364 (mmm) REVERT: A 52 MET cc_start: 0.7122 (mmt) cc_final: 0.6902 (mmt) REVERT: A 70 MET cc_start: 0.8341 (tpp) cc_final: 0.7836 (tpp) REVERT: C 41 MET cc_start: 0.8577 (mmm) cc_final: 0.8311 (mtp) REVERT: C 56 ASP cc_start: 0.7417 (m-30) cc_final: 0.6964 (t70) REVERT: E 1 MET cc_start: 0.5752 (ppp) cc_final: 0.5500 (ppp) REVERT: E 18 GLU cc_start: 0.8413 (pp20) cc_final: 0.8207 (pp20) REVERT: E 83 ILE cc_start: 0.9202 (mm) cc_final: 0.8908 (tp) REVERT: E 130 GLU cc_start: 0.8808 (tp30) cc_final: 0.8462 (tp30) REVERT: E 138 LEU cc_start: 0.7555 (tp) cc_final: 0.6966 (tp) REVERT: F 113 HIS cc_start: 0.8536 (p-80) cc_final: 0.8260 (p-80) REVERT: F 163 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7469 (Cg_endo) REVERT: G 50 MET cc_start: 0.8791 (mtp) cc_final: 0.8572 (ttm) REVERT: G 68 LEU cc_start: 0.8312 (mp) cc_final: 0.7933 (tp) REVERT: G 105 PHE cc_start: 0.7595 (m-80) cc_final: 0.7166 (m-80) REVERT: G 129 LEU cc_start: 0.8684 (mm) cc_final: 0.8452 (mp) REVERT: G 139 MET cc_start: 0.7564 (tpp) cc_final: 0.7105 (tpt) REVERT: G 148 PHE cc_start: 0.8829 (m-80) cc_final: 0.8550 (m-80) REVERT: H 16 TYR cc_start: 0.8243 (p90) cc_final: 0.7779 (p90) REVERT: H 124 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8200 (tptt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2167 time to fit residues: 36.5173 Evaluate side-chains 84 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10683 Z= 0.191 Angle : 0.676 7.807 14450 Z= 0.358 Chirality : 0.046 0.218 1631 Planarity : 0.004 0.038 1849 Dihedral : 6.167 66.625 1405 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.41 (0.23), residues: 1274 helix: 0.20 (0.22), residues: 519 sheet: -1.00 (0.35), residues: 210 loop : -2.01 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 100 HIS 0.005 0.001 HIS B 11 PHE 0.016 0.002 PHE C 140 TYR 0.038 0.002 TYR B 32 ARG 0.006 0.000 ARG F 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8721 (mmm) cc_final: 0.8398 (mmm) REVERT: A 70 MET cc_start: 0.8349 (tpp) cc_final: 0.7843 (tpp) REVERT: C 41 MET cc_start: 0.8584 (mmm) cc_final: 0.8332 (mtp) REVERT: C 56 ASP cc_start: 0.7413 (m-30) cc_final: 0.6982 (t70) REVERT: E 1 MET cc_start: 0.5731 (ppp) cc_final: 0.5471 (ppp) REVERT: E 18 GLU cc_start: 0.8355 (pp20) cc_final: 0.8152 (pp20) REVERT: E 83 ILE cc_start: 0.9175 (mm) cc_final: 0.8888 (tp) REVERT: F 113 HIS cc_start: 0.8525 (p-80) cc_final: 0.8255 (p-80) REVERT: F 163 PRO cc_start: 0.7601 (Cg_exo) cc_final: 0.7367 (Cg_endo) REVERT: G 50 MET cc_start: 0.8656 (mtp) cc_final: 0.8449 (ttm) REVERT: G 105 PHE cc_start: 0.7555 (m-80) cc_final: 0.7100 (m-80) REVERT: G 129 LEU cc_start: 0.8619 (mm) cc_final: 0.8404 (mp) REVERT: G 139 MET cc_start: 0.7576 (tpp) cc_final: 0.7131 (tpt) REVERT: G 148 PHE cc_start: 0.8826 (m-80) cc_final: 0.8403 (m-80) REVERT: H 16 TYR cc_start: 0.8209 (p90) cc_final: 0.7757 (p90) REVERT: H 124 LYS cc_start: 0.8407 (mmtm) cc_final: 0.8206 (tptt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2043 time to fit residues: 35.4609 Evaluate side-chains 81 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10683 Z= 0.183 Angle : 0.674 7.397 14450 Z= 0.357 Chirality : 0.046 0.202 1631 Planarity : 0.004 0.038 1849 Dihedral : 6.122 66.357 1405 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.32 (0.23), residues: 1274 helix: 0.26 (0.23), residues: 519 sheet: -0.75 (0.35), residues: 209 loop : -2.04 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 PHE 0.023 0.002 PHE D 186 TYR 0.026 0.002 TYR G 48 ARG 0.004 0.000 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8728 (mmm) cc_final: 0.8398 (mmm) REVERT: A 70 MET cc_start: 0.8232 (tpp) cc_final: 0.7756 (tpp) REVERT: C 41 MET cc_start: 0.8574 (mmm) cc_final: 0.8294 (mtp) REVERT: C 56 ASP cc_start: 0.7321 (m-30) cc_final: 0.6888 (t70) REVERT: E 1 MET cc_start: 0.5554 (ppp) cc_final: 0.5286 (ppp) REVERT: E 83 ILE cc_start: 0.9176 (mm) cc_final: 0.8930 (tp) REVERT: F 113 HIS cc_start: 0.8520 (p-80) cc_final: 0.8250 (p-80) REVERT: F 163 PRO cc_start: 0.7590 (Cg_exo) cc_final: 0.7349 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9093 (t0) cc_final: 0.8767 (t0) REVERT: G 50 MET cc_start: 0.8692 (mtp) cc_final: 0.8400 (ttm) REVERT: G 105 PHE cc_start: 0.7545 (m-80) cc_final: 0.7140 (m-80) REVERT: G 129 LEU cc_start: 0.8622 (mm) cc_final: 0.8387 (mp) REVERT: G 139 MET cc_start: 0.7641 (tpp) cc_final: 0.7130 (tpt) REVERT: G 148 PHE cc_start: 0.8784 (m-80) cc_final: 0.8470 (m-80) REVERT: H 16 TYR cc_start: 0.8293 (p90) cc_final: 0.7852 (p90) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2058 time to fit residues: 36.4502 Evaluate side-chains 80 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10683 Z= 0.188 Angle : 0.673 9.347 14450 Z= 0.354 Chirality : 0.046 0.197 1631 Planarity : 0.004 0.043 1849 Dihedral : 5.990 70.865 1405 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1274 helix: 0.30 (0.23), residues: 519 sheet: -0.59 (0.36), residues: 209 loop : -2.01 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 PHE 0.018 0.001 PHE B 35 TYR 0.034 0.002 TYR B 32 ARG 0.005 0.000 ARG E 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8762 (mmm) cc_final: 0.8443 (mmm) REVERT: A 52 MET cc_start: 0.7093 (mmt) cc_final: 0.6881 (mmt) REVERT: A 70 MET cc_start: 0.8247 (tpp) cc_final: 0.7783 (tpp) REVERT: C 41 MET cc_start: 0.8618 (mmm) cc_final: 0.8358 (mtp) REVERT: C 56 ASP cc_start: 0.7222 (m-30) cc_final: 0.6832 (t70) REVERT: D 69 MET cc_start: 0.7110 (pmm) cc_final: 0.6740 (pmm) REVERT: D 105 THR cc_start: 0.8639 (p) cc_final: 0.8369 (t) REVERT: E 1 MET cc_start: 0.5553 (ppp) cc_final: 0.5286 (ppp) REVERT: E 18 GLU cc_start: 0.8532 (pp20) cc_final: 0.8290 (pp20) REVERT: E 83 ILE cc_start: 0.9182 (mm) cc_final: 0.8934 (tp) REVERT: F 113 HIS cc_start: 0.8498 (p-80) cc_final: 0.8218 (p-80) REVERT: F 163 PRO cc_start: 0.7593 (Cg_exo) cc_final: 0.7349 (Cg_endo) REVERT: F 182 ASP cc_start: 0.9116 (t0) cc_final: 0.8752 (t0) REVERT: G 105 PHE cc_start: 0.7562 (m-80) cc_final: 0.7149 (m-80) REVERT: G 129 LEU cc_start: 0.8588 (mm) cc_final: 0.8365 (mp) REVERT: G 139 MET cc_start: 0.7586 (tpp) cc_final: 0.7151 (tpt) REVERT: G 148 PHE cc_start: 0.8823 (m-80) cc_final: 0.8504 (m-80) REVERT: H 16 TYR cc_start: 0.8295 (p90) cc_final: 0.7889 (p90) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2167 time to fit residues: 35.3053 Evaluate side-chains 85 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.0060 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS ** F 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.041674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.034209 restraints weight = 112096.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.035170 restraints weight = 82771.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.035914 restraints weight = 64757.617| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10683 Z= 0.182 Angle : 0.678 8.763 14450 Z= 0.358 Chirality : 0.046 0.299 1631 Planarity : 0.005 0.083 1849 Dihedral : 5.880 66.604 1405 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.18 (0.24), residues: 1274 helix: 0.33 (0.23), residues: 518 sheet: -0.55 (0.37), residues: 209 loop : -1.98 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 94 HIS 0.006 0.001 HIS B 11 PHE 0.020 0.001 PHE B 35 TYR 0.027 0.002 TYR G 48 ARG 0.013 0.001 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.04 seconds wall clock time: 39 minutes 1.53 seconds (2341.53 seconds total)