Starting phenix.real_space_refine on Wed Sep 25 08:35:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6skk_10226/09_2024/6skk_10226.cif" } resolution = 3.6 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= 0.001 sd= 0.012 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 78 5.16 5 C 6506 2.51 5 N 1806 2.21 5 O 1938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 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: 10328 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "C" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "D" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "F" Number of atoms: 1724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Conformer: "B" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} bond proxies already assigned to first conformer: 1745 Time building chain proxies: 9.00, per 1000 atoms: 0.87 Number of scatterers: 10328 At special positions: 0 Unit cell: (109.18, 117.66, 80.56, 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 78 16.00 O 1938 8.00 N 1806 7.00 C 6506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.03 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: 2.60 Conformation dependent library (CDL) restraints added in 2.6 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 5 sheets defined 67.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.791A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.803A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.008A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.536A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.871A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.766A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 145 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.905A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET E 214 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.526A pdb=" N LEU F 20 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.362A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.922A pdb=" N CYS F 218 " --> pdb=" O MET F 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.669A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.664A pdb=" N VAL E 3 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 11 " --> pdb=" O VAL E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.541A pdb=" N VAL F 3 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL F 11 " --> pdb=" O VAL F 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 595 hydrogen bonds defined for protein. 1776 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: 2.75 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3219 1.34 - 1.46: 1521 1.46 - 1.58: 5676 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 10560 Sorted by residual: bond pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta sigma weight residual 1.456 1.485 -0.029 8.70e-03 1.32e+04 1.13e+01 bond pdb=" N VAL B 36 " pdb=" CA VAL B 36 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL E 36 " pdb=" CA VAL E 36 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.41e+00 bond pdb=" N VAL D 36 " pdb=" CA VAL D 36 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.40e+00 ... (remaining 10555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 13490 1.12 - 2.25: 655 2.25 - 3.37: 181 3.37 - 4.50: 28 4.50 - 5.62: 8 Bond angle restraints: 14362 Sorted by residual: angle pdb=" C ALA F 31 " pdb=" CA ALA F 31 " pdb=" CB ALA F 31 " ideal model delta sigma weight residual 116.54 110.92 5.62 1.15e+00 7.56e-01 2.39e+01 angle pdb=" CA GLY D 61 " pdb=" C GLY D 61 " pdb=" O GLY D 61 " ideal model delta sigma weight residual 122.78 117.66 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" CA ALA F 31 " pdb=" C ALA F 31 " pdb=" N PHE F 32 " ideal model delta sigma weight residual 119.52 116.58 2.94 7.90e-01 1.60e+00 1.38e+01 angle pdb=" CA SER B 33 " pdb=" C SER B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 117.68 120.29 -2.61 7.10e-01 1.98e+00 1.35e+01 angle pdb=" C ALA B 31 " pdb=" CA ALA B 31 " pdb=" CB ALA B 31 " ideal model delta sigma weight residual 116.63 112.60 4.03 1.16e+00 7.43e-01 1.21e+01 ... (remaining 14357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6009 17.93 - 35.86: 400 35.86 - 53.79: 94 53.79 - 71.72: 11 71.72 - 89.65: 8 Dihedral angle restraints: 6522 sinusoidal: 2696 harmonic: 3826 Sorted by residual: dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -134.76 48.76 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB GLU B 28 " pdb=" CG GLU B 28 " pdb=" CD GLU B 28 " pdb=" OE1 GLU B 28 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 213 " pdb=" CG GLU A 213 " pdb=" CD GLU A 213 " pdb=" OE1 GLU A 213 " ideal model delta sinusoidal sigma weight residual 0.00 -89.55 89.55 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1131 0.036 - 0.072: 338 0.072 - 0.109: 110 0.109 - 0.145: 21 0.145 - 0.181: 6 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA VAL D 36 " pdb=" N VAL D 36 " pdb=" C VAL D 36 " pdb=" CB VAL D 36 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA VAL E 36 " pdb=" N VAL E 36 " pdb=" C VAL E 36 " pdb=" CB VAL E 36 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 1603 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 28 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C GLU E 28 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU E 28 " 0.030 2.00e-02 2.50e+03 pdb=" N GLU E 29 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " -0.023 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLU A 28 " 0.080 2.00e-02 2.50e+03 pdb=" O GLU A 28 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU A 29 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 28 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C GLU D 28 " -0.069 2.00e-02 2.50e+03 pdb=" O GLU D 28 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU D 29 " 0.023 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3241 2.83 - 3.35: 10396 3.35 - 3.87: 16612 3.87 - 4.38: 18319 4.38 - 4.90: 30470 Nonbonded interactions: 79038 Sorted by model distance: nonbonded pdb=" O THR C 54 " pdb=" OG1 THR C 58 " model vdw 2.319 3.040 nonbonded pdb=" O ILE F 115 " pdb=" OG1 THR F 119 " model vdw 2.327 3.040 nonbonded pdb=" O GLY D 156 " pdb=" ND2 ASN D 195 " model vdw 2.339 3.120 nonbonded pdb=" NE2 GLN E 155 " pdb=" O GLU E 159 " model vdw 2.351 3.120 nonbonded pdb=" OG SER B 102 " pdb=" OG1 THR B 107 " model vdw 2.357 3.040 ... (remaining 79033 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' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'B' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'C' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'D' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'E' and (resid 1 through 17 or resid 19 through 220)) selection = (chain 'F' and (resid 1 through 17 or resid 19 through 220)) } 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=0.50 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: 0.210 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.390 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.003 0.038 10560 Z= 0.227 Angle : 0.605 5.622 14362 Z= 0.392 Chirality : 0.041 0.181 1606 Planarity : 0.004 0.046 1880 Dihedral : 12.957 89.647 4024 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: -1.14 (0.21), residues: 1312 helix: -0.47 (0.16), residues: 862 sheet: -3.37 (0.46), residues: 54 loop : -0.61 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 80 HIS 0.002 0.001 HIS D 62 PHE 0.004 0.001 PHE F 40 TYR 0.014 0.001 TYR F 130 ARG 0.004 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.6854 (mtp) cc_final: 0.6549 (mtp) REVERT: A 118 MET cc_start: 0.8323 (mtm) cc_final: 0.7783 (mtp) REVERT: A 144 MET cc_start: 0.8019 (ttp) cc_final: 0.7694 (ttt) REVERT: B 55 MET cc_start: 0.8091 (mtp) cc_final: 0.7777 (mtp) REVERT: B 144 MET cc_start: 0.7663 (ttt) cc_final: 0.7371 (ttm) REVERT: C 25 LYS cc_start: 0.8061 (mttt) cc_final: 0.7720 (mttm) REVERT: C 182 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8128 (mtpp) REVERT: D 66 MET cc_start: 0.7990 (mmm) cc_final: 0.7469 (mmm) REVERT: D 118 MET cc_start: 0.8197 (mtm) cc_final: 0.7917 (mtp) REVERT: D 144 MET cc_start: 0.7953 (ttp) cc_final: 0.7064 (ttp) REVERT: D 203 LYS cc_start: 0.7344 (mmmt) cc_final: 0.7038 (tttm) REVERT: E 25 LYS cc_start: 0.8211 (mttt) cc_final: 0.7851 (mttm) REVERT: E 66 MET cc_start: 0.8959 (mmm) cc_final: 0.8700 (mmt) REVERT: F 12 HIS cc_start: 0.8107 (t70) cc_final: 0.7896 (t-90) REVERT: F 182 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8155 (mtpt) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2781 time to fit residues: 125.9909 Evaluate side-chains 243 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 34 optimal weight: 0.0030 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 overall best weight: 1.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 7 GLN A 183 ASN A 195 ASN B 9 GLN B 53 ASN B 179 GLN B 183 ASN B 219 GLN C 21 ASN C 219 GLN D 4 GLN ** D 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 95 GLN D 195 ASN E 9 GLN E 53 ASN E 219 GLN F 9 GLN F 21 ASN F 95 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10560 Z= 0.207 Angle : 0.592 9.911 14362 Z= 0.304 Chirality : 0.043 0.165 1606 Planarity : 0.005 0.044 1880 Dihedral : 3.795 18.399 1410 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.69 % Allowed : 14.30 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.26 (0.23), residues: 1312 helix: 0.56 (0.18), residues: 868 sheet: -2.97 (0.52), residues: 54 loop : 0.07 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.009 0.001 PHE C 40 TYR 0.016 0.002 TYR F 130 ARG 0.004 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 261 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7271 (tpt-90) cc_final: 0.6868 (tpt90) REVERT: A 118 MET cc_start: 0.8415 (mtm) cc_final: 0.7915 (mtp) REVERT: B 55 MET cc_start: 0.8232 (mtp) cc_final: 0.7906 (mtp) REVERT: B 144 MET cc_start: 0.7578 (ttt) cc_final: 0.7371 (ttm) REVERT: C 25 LYS cc_start: 0.8139 (mttt) cc_final: 0.7790 (mttm) REVERT: C 28 GLU cc_start: 0.6346 (mm-30) cc_final: 0.6041 (mm-30) REVERT: C 66 MET cc_start: 0.8521 (mmm) cc_final: 0.8158 (mmt) REVERT: C 182 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8169 (mtpt) REVERT: C 214 MET cc_start: 0.8361 (tpp) cc_final: 0.8109 (tpt) REVERT: D 118 MET cc_start: 0.8322 (mtm) cc_final: 0.7886 (mtp) REVERT: D 144 MET cc_start: 0.7571 (ttp) cc_final: 0.7295 (ttp) REVERT: D 203 LYS cc_start: 0.7360 (mmmt) cc_final: 0.7019 (tttm) REVERT: E 114 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 117 TRP cc_start: 0.7994 (m-10) cc_final: 0.7754 (m-10) REVERT: F 25 LYS cc_start: 0.8295 (mttt) cc_final: 0.7952 (mttp) outliers start: 17 outliers final: 10 residues processed: 270 average time/residue: 0.2872 time to fit residues: 102.8591 Evaluate side-chains 242 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 231 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.0470 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 195 ASN B 179 GLN B 183 ASN D 12 HIS D 195 ASN F 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10560 Z= 0.194 Angle : 0.560 6.922 14362 Z= 0.290 Chirality : 0.043 0.287 1606 Planarity : 0.005 0.053 1880 Dihedral : 3.824 18.363 1410 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.87 % Allowed : 16.16 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.75 (0.24), residues: 1312 helix: 0.91 (0.18), residues: 868 sheet: -2.68 (0.57), residues: 54 loop : 0.32 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.014 0.001 PHE B 161 TYR 0.012 0.002 TYR F 130 ARG 0.004 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8308 (mtm) cc_final: 0.7832 (mtp) REVERT: B 55 MET cc_start: 0.8172 (mtp) cc_final: 0.7890 (mtp) REVERT: B 97 ARG cc_start: 0.8406 (ptt-90) cc_final: 0.8155 (ptt-90) REVERT: C 25 LYS cc_start: 0.8078 (mttt) cc_final: 0.7710 (mttm) REVERT: C 117 TRP cc_start: 0.7946 (m-90) cc_final: 0.7664 (m-90) REVERT: C 182 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8248 (mtpp) REVERT: D 100 ARG cc_start: 0.7269 (tpt-90) cc_final: 0.6601 (tpt90) REVERT: D 118 MET cc_start: 0.8324 (mtm) cc_final: 0.7904 (mtp) REVERT: D 144 MET cc_start: 0.7802 (ttp) cc_final: 0.7563 (ttp) REVERT: D 149 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8129 (t) REVERT: D 203 LYS cc_start: 0.7379 (mmmt) cc_final: 0.7007 (tttm) REVERT: E 151 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7529 (mm) REVERT: F 25 LYS cc_start: 0.8195 (mttt) cc_final: 0.7884 (mttp) REVERT: F 44 SER cc_start: 0.8791 (p) cc_final: 0.8543 (t) outliers start: 19 outliers final: 10 residues processed: 257 average time/residue: 0.2562 time to fit residues: 87.7355 Evaluate side-chains 237 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 225 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 0.0060 overall best weight: 2.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 195 ASN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10560 Z= 0.227 Angle : 0.595 11.160 14362 Z= 0.307 Chirality : 0.043 0.259 1606 Planarity : 0.005 0.051 1880 Dihedral : 3.907 18.081 1410 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.31 % Allowed : 16.87 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.86 (0.24), residues: 1312 helix: 0.98 (0.18), residues: 882 sheet: -2.54 (0.60), residues: 54 loop : 0.36 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 117 HIS 0.007 0.001 HIS C 12 PHE 0.008 0.001 PHE B 161 TYR 0.011 0.002 TYR F 130 ARG 0.004 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 241 time to evaluate : 1.204 Fit side-chains REVERT: A 100 ARG cc_start: 0.7227 (tpt-90) cc_final: 0.6469 (tpt90) REVERT: A 118 MET cc_start: 0.8322 (mtm) cc_final: 0.7791 (mtp) REVERT: A 172 LEU cc_start: 0.8972 (tp) cc_final: 0.8746 (tt) REVERT: B 35 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6804 (pm20) REVERT: B 55 MET cc_start: 0.8244 (mtp) cc_final: 0.7985 (mtp) REVERT: B 98 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: C 25 LYS cc_start: 0.8065 (mttt) cc_final: 0.7661 (mttm) REVERT: C 100 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7482 (ttp-110) REVERT: C 182 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8226 (mtpp) REVERT: D 118 MET cc_start: 0.8395 (mtm) cc_final: 0.7951 (mtp) REVERT: D 144 MET cc_start: 0.7756 (ttp) cc_final: 0.7474 (ttp) REVERT: D 145 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: D 149 SER cc_start: 0.8368 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 203 LYS cc_start: 0.7372 (mmmt) cc_final: 0.6976 (tttm) REVERT: E 114 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: E 151 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7617 (mm) REVERT: F 25 LYS cc_start: 0.8177 (mttt) cc_final: 0.7533 (mttm) REVERT: F 28 GLU cc_start: 0.6575 (mm-30) cc_final: 0.5991 (mm-30) outliers start: 24 outliers final: 14 residues processed: 255 average time/residue: 0.2542 time to fit residues: 86.9142 Evaluate side-chains 244 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 88 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 195 ASN F 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10560 Z= 0.254 Angle : 0.619 10.198 14362 Z= 0.317 Chirality : 0.044 0.237 1606 Planarity : 0.005 0.050 1880 Dihedral : 4.019 18.437 1410 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.40 % Allowed : 17.76 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.90 (0.24), residues: 1312 helix: 1.01 (0.18), residues: 882 sheet: -2.40 (0.62), residues: 54 loop : 0.37 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 117 HIS 0.006 0.001 HIS C 12 PHE 0.015 0.001 PHE E 161 TYR 0.010 0.002 TYR F 130 ARG 0.006 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 1.287 Fit side-chains REVERT: A 118 MET cc_start: 0.8307 (mtm) cc_final: 0.7731 (mtp) REVERT: B 35 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: B 55 MET cc_start: 0.8315 (mtp) cc_final: 0.8042 (mtp) REVERT: B 98 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: C 100 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7342 (ttp-110) REVERT: C 117 TRP cc_start: 0.8106 (m-90) cc_final: 0.7824 (m-90) REVERT: C 133 TRP cc_start: 0.7810 (m-10) cc_final: 0.7026 (m-10) REVERT: D 100 ARG cc_start: 0.7362 (tpt-90) cc_final: 0.6965 (tpt-90) REVERT: D 118 MET cc_start: 0.8423 (mtm) cc_final: 0.7964 (mtp) REVERT: D 145 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: D 149 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8145 (t) REVERT: D 203 LYS cc_start: 0.7398 (mmmt) cc_final: 0.6993 (tttm) REVERT: E 114 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: E 151 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7638 (mm) REVERT: F 28 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6077 (mm-30) outliers start: 25 outliers final: 16 residues processed: 246 average time/residue: 0.2652 time to fit residues: 85.9977 Evaluate side-chains 233 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 145 TYR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10560 Z= 0.418 Angle : 0.712 10.376 14362 Z= 0.373 Chirality : 0.048 0.209 1606 Planarity : 0.006 0.053 1880 Dihedral : 4.414 19.291 1410 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.22 % Allowed : 18.83 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.49 (0.23), residues: 1312 helix: 0.69 (0.18), residues: 878 sheet: -2.38 (0.63), residues: 54 loop : 0.19 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 117 HIS 0.006 0.002 HIS C 12 PHE 0.013 0.002 PHE D 32 TYR 0.017 0.003 TYR D 130 ARG 0.006 0.001 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 1.262 Fit side-chains REVERT: A 29 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7211 (mm-30) REVERT: A 118 MET cc_start: 0.8282 (mtm) cc_final: 0.7775 (mtp) REVERT: B 35 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: B 55 MET cc_start: 0.8476 (mtp) cc_final: 0.8254 (mtp) REVERT: B 98 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: C 100 ARG cc_start: 0.7886 (ptm160) cc_final: 0.7356 (ttp-110) REVERT: C 114 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 117 TRP cc_start: 0.8344 (m-90) cc_final: 0.8126 (m-90) REVERT: C 133 TRP cc_start: 0.7956 (m-10) cc_final: 0.7190 (m-10) REVERT: C 182 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8344 (mtpp) REVERT: D 100 ARG cc_start: 0.7377 (tpt-90) cc_final: 0.6645 (tpt-90) REVERT: D 118 MET cc_start: 0.8553 (mtm) cc_final: 0.8129 (mtp) REVERT: D 203 LYS cc_start: 0.7392 (mmmt) cc_final: 0.6976 (tttm) REVERT: E 114 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: E 151 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7702 (mm) REVERT: F 25 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7444 (ttpp) REVERT: F 143 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7384 (mmm160) REVERT: F 182 LYS cc_start: 0.8473 (mmmt) cc_final: 0.8095 (mmmt) outliers start: 23 outliers final: 13 residues processed: 246 average time/residue: 0.2757 time to fit residues: 89.9783 Evaluate side-chains 241 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 214 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN D 179 GLN D 195 ASN F 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10560 Z= 0.264 Angle : 0.629 9.205 14362 Z= 0.325 Chirality : 0.045 0.184 1606 Planarity : 0.005 0.051 1880 Dihedral : 4.284 20.884 1410 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.78 % Allowed : 19.72 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.79 (0.24), residues: 1312 helix: 0.97 (0.18), residues: 874 sheet: -2.35 (0.61), residues: 54 loop : 0.19 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 117 HIS 0.005 0.001 HIS C 12 PHE 0.010 0.001 PHE E 161 TYR 0.011 0.002 TYR A 130 ARG 0.006 0.001 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7162 (mm-30) REVERT: A 118 MET cc_start: 0.8062 (mtm) cc_final: 0.7674 (mtp) REVERT: B 35 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: B 55 MET cc_start: 0.8413 (mtp) cc_final: 0.8103 (mtp) REVERT: B 98 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: C 25 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7828 (ttmt) REVERT: C 100 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7333 (ttp-110) REVERT: C 114 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: C 133 TRP cc_start: 0.7854 (m-10) cc_final: 0.7052 (m-10) REVERT: C 182 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8476 (mtpt) REVERT: D 118 MET cc_start: 0.8299 (mtm) cc_final: 0.7923 (mtp) REVERT: D 143 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7602 (mtm180) REVERT: D 149 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8172 (t) REVERT: D 179 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5578 (mm110) REVERT: D 203 LYS cc_start: 0.7395 (mmmt) cc_final: 0.7015 (tttm) REVERT: E 114 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: E 151 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7709 (mm) REVERT: F 25 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7236 (ttpp) REVERT: F 143 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7373 (mmm160) outliers start: 18 outliers final: 10 residues processed: 241 average time/residue: 0.2529 time to fit residues: 81.1748 Evaluate side-chains 232 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 215 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 214 MET Chi-restraints excluded: chain F residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 111 optimal weight: 0.0870 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10560 Z= 0.196 Angle : 0.631 11.222 14362 Z= 0.323 Chirality : 0.043 0.172 1606 Planarity : 0.005 0.049 1880 Dihedral : 4.179 20.739 1410 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.69 % Allowed : 19.98 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1312 helix: 1.09 (0.18), residues: 877 sheet: -2.18 (0.62), residues: 54 loop : 0.35 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.010 0.001 PHE E 161 TYR 0.010 0.001 TYR A 169 ARG 0.006 0.000 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.234 Fit side-chains REVERT: A 118 MET cc_start: 0.8015 (mtm) cc_final: 0.7628 (mtp) REVERT: B 55 MET cc_start: 0.8285 (mtp) cc_final: 0.7938 (mtp) REVERT: B 98 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: B 110 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6458 (p) REVERT: C 25 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7433 (tttp) REVERT: C 100 ARG cc_start: 0.7785 (ptm160) cc_final: 0.7300 (ttp-110) REVERT: C 114 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: C 117 TRP cc_start: 0.8010 (m-90) cc_final: 0.7681 (m-90) REVERT: C 133 TRP cc_start: 0.7754 (m-10) cc_final: 0.6973 (m-10) REVERT: C 182 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8424 (mtmt) REVERT: D 99 PRO cc_start: 0.6317 (Cg_exo) cc_final: 0.5855 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7316 (tpt-90) cc_final: 0.6750 (tpt90) REVERT: D 118 MET cc_start: 0.8325 (mtm) cc_final: 0.7958 (mtp) REVERT: D 149 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8113 (t) REVERT: D 179 GLN cc_start: 0.6237 (OUTLIER) cc_final: 0.5455 (mm110) REVERT: D 203 LYS cc_start: 0.7451 (mmmt) cc_final: 0.7068 (tttm) REVERT: E 114 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: E 151 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7748 (mm) REVERT: F 25 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7301 (ttpp) REVERT: F 28 GLU cc_start: 0.6757 (mm-30) cc_final: 0.5930 (mm-30) REVERT: F 143 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7452 (mmm160) REVERT: F 182 LYS cc_start: 0.8256 (mmmt) cc_final: 0.7921 (mmmt) outliers start: 17 outliers final: 7 residues processed: 245 average time/residue: 0.2679 time to fit residues: 86.6435 Evaluate side-chains 236 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 222 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10560 Z= 0.235 Angle : 0.645 11.184 14362 Z= 0.326 Chirality : 0.044 0.171 1606 Planarity : 0.005 0.053 1880 Dihedral : 4.161 20.582 1410 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 19.72 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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 (0.24), residues: 1312 helix: 1.06 (0.18), residues: 880 sheet: -2.01 (0.62), residues: 54 loop : 0.34 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.016 0.001 PHE C 168 TYR 0.026 0.002 TYR A 169 ARG 0.007 0.001 ARG C 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 1.111 Fit side-chains REVERT: A 29 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 118 MET cc_start: 0.8068 (mtm) cc_final: 0.7675 (mtp) REVERT: B 55 MET cc_start: 0.8311 (mtp) cc_final: 0.7992 (mtp) REVERT: B 98 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: B 151 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (mm) REVERT: C 25 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7358 (ttpp) REVERT: C 100 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7300 (ttp-110) REVERT: C 114 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: C 117 TRP cc_start: 0.8061 (m-90) cc_final: 0.7823 (m-90) REVERT: C 133 TRP cc_start: 0.7804 (m-10) cc_final: 0.6796 (m100) REVERT: C 182 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8164 (mtmt) REVERT: D 99 PRO cc_start: 0.6388 (Cg_exo) cc_final: 0.5926 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7257 (tpt-90) cc_final: 0.6873 (tpt90) REVERT: D 118 MET cc_start: 0.8378 (mtm) cc_final: 0.7887 (mtp) REVERT: D 149 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8107 (t) REVERT: D 179 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.6022 (mm-40) REVERT: D 203 LYS cc_start: 0.7453 (mmmt) cc_final: 0.7077 (tttm) REVERT: E 114 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: E 151 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7709 (mm) REVERT: F 25 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7253 (ttpp) REVERT: F 143 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7530 (mmm160) REVERT: F 215 MET cc_start: 0.7675 (ptp) cc_final: 0.7362 (mpp) outliers start: 20 outliers final: 11 residues processed: 235 average time/residue: 0.2666 time to fit residues: 83.1920 Evaluate side-chains 239 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10560 Z= 0.340 Angle : 0.705 11.290 14362 Z= 0.361 Chirality : 0.046 0.185 1606 Planarity : 0.005 0.054 1880 Dihedral : 4.329 21.074 1410 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.87 % Allowed : 20.60 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.74 (0.23), residues: 1312 helix: 0.94 (0.18), residues: 864 sheet: -2.28 (1.02), residues: 18 loop : -0.12 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.009 0.002 PHE C 168 TYR 0.025 0.002 TYR D 169 ARG 0.006 0.001 ARG C 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.103 Fit side-chains REVERT: A 29 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7174 (mm-30) REVERT: A 118 MET cc_start: 0.8247 (mtm) cc_final: 0.7750 (mtp) REVERT: B 55 MET cc_start: 0.8358 (mtp) cc_final: 0.8118 (mtp) REVERT: B 98 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: B 151 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7545 (mm) REVERT: C 25 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7389 (ttpp) REVERT: C 100 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7297 (ttp-110) REVERT: C 114 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.6751 (mp-120) REVERT: C 117 TRP cc_start: 0.8086 (m-90) cc_final: 0.7827 (m-90) REVERT: C 133 TRP cc_start: 0.7855 (m-10) cc_final: 0.6883 (m100) REVERT: C 215 MET cc_start: 0.7754 (ptp) cc_final: 0.7551 (mpp) REVERT: D 99 PRO cc_start: 0.6454 (Cg_exo) cc_final: 0.5994 (Cg_endo) REVERT: D 100 ARG cc_start: 0.7311 (tpt-90) cc_final: 0.6928 (tpt90) REVERT: D 118 MET cc_start: 0.8491 (mtm) cc_final: 0.8036 (mtp) REVERT: D 149 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 179 GLN cc_start: 0.6333 (OUTLIER) cc_final: 0.5943 (mm-40) REVERT: D 203 LYS cc_start: 0.7460 (mmmt) cc_final: 0.7073 (tttm) REVERT: E 114 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: E 151 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7685 (mm) REVERT: F 25 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7321 (ttpp) REVERT: F 143 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7436 (mmm160) REVERT: F 215 MET cc_start: 0.7695 (ptp) cc_final: 0.7453 (mpp) outliers start: 19 outliers final: 9 residues processed: 226 average time/residue: 0.2611 time to fit residues: 78.5947 Evaluate side-chains 229 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 GLN F 21 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.137502 restraints weight = 28646.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142412 restraints weight = 16750.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142743 restraints weight = 11959.545| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10560 Z= 0.194 Angle : 0.645 11.434 14362 Z= 0.326 Chirality : 0.044 0.167 1606 Planarity : 0.005 0.052 1880 Dihedral : 4.179 21.060 1410 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 20.69 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.16 % 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: 0.99 (0.24), residues: 1312 helix: 1.15 (0.18), residues: 866 sheet: -1.82 (1.14), residues: 18 loop : -0.06 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP C 117 HIS 0.005 0.001 HIS C 12 PHE 0.015 0.001 PHE C 168 TYR 0.020 0.001 TYR D 169 ARG 0.006 0.000 ARG E 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2368.26 seconds wall clock time: 42 minutes 42.16 seconds (2562.16 seconds total)