Starting phenix.real_space_refine on Tue Aug 4 19:32:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ruh_54272/08_2026/9ruh_54272.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3968 2.51 5 N 1053 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6257 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1667 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 13, 'TRANS': 205} Chain breaks: 1 Chain: "L" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1463 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 1 Chain: "A" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1458 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Time building chain proxies: 1.32, per 1000 atoms: 0.21 Number of scatterers: 6257 At special positions: 0 Unit cell: (67.32, 82.11, 131.58, 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 24 16.00 O 1212 8.00 N 1053 7.00 C 3968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 166 " 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: 0.52 Conformation dependent library (CDL) restraints added in 363.2 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 13.7% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 198 through 202 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.610A pdb=" N GLN B 64 " --> pdb=" O TYR B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 removed outlier: 3.873A pdb=" N LEU B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N HIS B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 58 through 80 removed outlier: 3.958A pdb=" N ALA A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.802A pdb=" N TYR H 32 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TRP H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN H 57 " --> pdb=" O TRP H 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.722A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 133 through 137 removed outlier: 6.234A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 133 through 137 removed outlier: 6.234A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 164 through 167 removed outlier: 3.776A pdb=" N THR H 164 " --> pdb=" O ASN H 212 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS H 209 " --> pdb=" O LYS H 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.601A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.022A pdb=" N VAL L 29 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N GLY L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.891A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.891A pdb=" N LEU L 11 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.576A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA L 132 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 147 through 152 removed outlier: 3.515A pdb=" N CYS L 196 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 49 removed outlier: 4.809A pdb=" N GLU B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR B 32 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS B 15 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER A 10 " --> pdb=" O CYS B 15 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE B 17 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL A 8 " --> pdb=" O PHE B 17 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS A 11 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU A 28 " --> pdb=" O CYS A 11 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 22 " --> pdb=" O GLN A 17 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLY A 23 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ASP A 38 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR A 25 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR A 36 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS A 27 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 103 removed outlier: 3.532A pdb=" N SER B 102 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 116 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 143 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 98 through 103 removed outlier: 3.532A pdb=" N SER B 102 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 116 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE B 155 " --> pdb=" O ASP B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 136 through 138 removed outlier: 4.343A pdb=" N TRP B 131 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.872A pdb=" N PHE A 148 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 136 " --> pdb=" O TYR A 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 91 through 96 removed outlier: 5.872A pdb=" N PHE A 148 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 129 through 131 removed outlier: 4.359A pdb=" N TRP A 124 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 164 " --> pdb=" O TRP A 181 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 792 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: 1.12 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1245 1.33 - 1.45: 1661 1.45 - 1.57: 3479 1.57 - 1.69: 0 1.69 - 1.82: 33 Bond restraints: 6418 Sorted by residual: bond pdb=" N PRO L 96 " pdb=" CD PRO L 96 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 8.98e+00 bond pdb=" C PHE H 159 " pdb=" N PRO H 160 " ideal model delta sigma weight residual 1.333 1.358 -0.026 1.17e-02 7.31e+03 4.84e+00 bond pdb=" C ALA L 93 " pdb=" O ALA L 93 " ideal model delta sigma weight residual 1.234 1.205 0.028 1.30e-02 5.92e+03 4.73e+00 bond pdb=" C GLU L 80 " pdb=" N PRO L 81 " ideal model delta sigma weight residual 1.335 1.362 -0.027 1.28e-02 6.10e+03 4.42e+00 bond pdb=" C GLU H 161 " pdb=" O GLU H 161 " ideal model delta sigma weight residual 1.244 1.227 0.016 9.80e-03 1.04e+04 2.82e+00 ... (remaining 6413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8494 2.00 - 4.00: 175 4.00 - 6.00: 51 6.00 - 7.99: 15 7.99 - 9.99: 11 Bond angle restraints: 8746 Sorted by residual: angle pdb=" C GLU L 80 " pdb=" N PRO L 81 " pdb=" CA PRO L 81 " ideal model delta sigma weight residual 119.28 113.92 5.36 1.10e+00 8.26e-01 2.38e+01 angle pdb=" CA PRO L 8 " pdb=" N PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 112.00 105.31 6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" C PHE H 159 " pdb=" N PRO H 160 " pdb=" CA PRO H 160 " ideal model delta sigma weight residual 119.90 114.90 5.00 1.05e+00 9.07e-01 2.27e+01 angle pdb=" N ASP B 152 " pdb=" CA ASP B 152 " pdb=" C ASP B 152 " ideal model delta sigma weight residual 110.80 101.21 9.59 2.13e+00 2.20e-01 2.03e+01 angle pdb=" N ALA B 86 " pdb=" CA ALA B 86 " pdb=" C ALA B 86 " ideal model delta sigma weight residual 110.80 119.96 -9.16 2.13e+00 2.20e-01 1.85e+01 ... (remaining 8741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3379 17.94 - 35.87: 315 35.87 - 53.81: 92 53.81 - 71.75: 14 71.75 - 89.69: 4 Dihedral angle restraints: 3804 sinusoidal: 1475 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -26.01 -59.99 1 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" CA PRO L 8 " pdb=" C PRO L 8 " pdb=" N GLY L 9 " pdb=" CA GLY L 9 " ideal model delta harmonic sigma weight residual -180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual -86.00 -123.70 37.70 1 1.00e+01 1.00e-02 2.00e+01 ... (remaining 3801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 821 0.068 - 0.136: 135 0.136 - 0.204: 9 0.204 - 0.272: 1 0.272 - 0.341: 2 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA MET L 97 " pdb=" N MET L 97 " pdb=" C MET L 97 " pdb=" CB MET L 97 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ASP H 157 " pdb=" N ASP H 157 " pdb=" C ASP H 157 " pdb=" CB ASP H 157 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA GLU H 161 " pdb=" N GLU H 161 " pdb=" C GLU H 161 " pdb=" CB GLU H 161 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 965 not shown) Planarity restraints: 1128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " -0.092 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO L 96 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.17e+01 pdb=" N PRO L 8 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 102 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 103 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.037 5.00e-02 4.00e+02 ... (remaining 1125 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 475 2.74 - 3.28: 5979 3.28 - 3.82: 10719 3.82 - 4.36: 12782 4.36 - 4.90: 22373 Nonbonded interactions: 52328 Sorted by model distance: nonbonded pdb=" OE1 GLU A 33 " pdb=" OG SER A 139 " model vdw 2.200 3.040 nonbonded pdb=" OG SER A 98 " pdb=" OD1 ASN A 106 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU L 107 " pdb=" OH TYR L 175 " model vdw 2.253 3.040 nonbonded pdb=" N GLN B 181 " pdb=" OE1 GLN B 181 " model vdw 2.262 3.120 nonbonded pdb=" NE1 TRP H 52 " pdb=" O ALA B 49 " model vdw 2.274 3.120 ... (remaining 52323 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6425 Z= 0.191 Angle : 0.816 9.993 8760 Z= 0.437 Chirality : 0.051 0.341 968 Planarity : 0.008 0.136 1128 Dihedral : 15.224 89.686 2287 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 0.43 % Allowed : 23.62 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.31), residues: 777 helix: 1.37 (0.62), residues: 70 sheet: 1.24 (0.30), residues: 304 loop : 1.13 (0.34), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 41 TYR 0.014 0.001 TYR H 59 PHE 0.028 0.002 PHE L 120 TRP 0.018 0.001 TRP L 150 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 ( 6418) covalent geometry : angle 0.81436 / 0.44 ( 8746) SS BOND : bond 0.00257 / 0.13 ( 7) SS BOND : angle 1.49634 / 0.81 ( 14) hydrogen bonds : bond 0.21930 / 14.88 ( 263) hydrogen bonds : angle 9.35354 / 6.51 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: H 184 GLN cc_start: 0.8504 (mt0) cc_final: 0.8295 (mt0) REVERT: L 82 GLU cc_start: 0.8433 (pp20) cc_final: 0.8034 (pp20) REVERT: L 83 ASP cc_start: 0.8707 (m-30) cc_final: 0.8208 (m-30) REVERT: L 145 GLU cc_start: 0.7791 (pp20) cc_final: 0.7446 (pp20) REVERT: L 185 LYS cc_start: 0.8974 (tppp) cc_final: 0.8751 (tppt) REVERT: L 197 GLU cc_start: 0.8794 (tp30) cc_final: 0.8567 (mm-30) REVERT: B 128 LYS cc_start: 0.9296 (mmmt) cc_final: 0.9065 (mtmt) REVERT: A 58 ASP cc_start: 0.8750 (t0) cc_final: 0.8527 (t0) outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.4709 time to fit residues: 73.3144 Evaluate side-chains 133 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 125 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 139 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN B 126 GLN B 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062160 restraints weight = 12035.473| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.84 r_work: 0.2741 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6425 Z= 0.226 Angle : 0.691 10.235 8760 Z= 0.347 Chirality : 0.047 0.141 968 Planarity : 0.005 0.075 1128 Dihedral : 7.231 159.795 871 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.35 % Allowed : 18.70 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.30), residues: 777 helix: 1.16 (0.59), residues: 71 sheet: 1.22 (0.28), residues: 315 loop : 0.87 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.013 0.001 TYR H 59 PHE 0.019 0.002 PHE L 84 TRP 0.009 0.001 TRP B 153 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 6418) covalent geometry : angle 0.69062 / 0.35 ( 8746) SS BOND : bond 0.00332 / 0.18 ( 7) SS BOND : angle 0.73113 / 0.37 ( 14) hydrogen bonds : bond 0.04014 / 2.72 ( 263) hydrogen bonds : angle 6.12852 / 4.25 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8378 (t0) cc_final: 0.7489 (t0) REVERT: H 76 LYS cc_start: 0.9547 (mtmp) cc_final: 0.8902 (mtmp) REVERT: H 212 ASN cc_start: 0.8330 (p0) cc_final: 0.8119 (p0) REVERT: H 214 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8890 (mmpt) REVERT: L 24 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8203 (ttm-80) REVERT: L 82 GLU cc_start: 0.8596 (pp20) cc_final: 0.8223 (pp20) REVERT: L 83 ASP cc_start: 0.8482 (m-30) cc_final: 0.7994 (m-30) REVERT: L 109 LYS cc_start: 0.9138 (tppp) cc_final: 0.8910 (ttpp) REVERT: L 145 GLU cc_start: 0.7807 (pp20) cc_final: 0.7517 (pp20) REVERT: L 149 GLN cc_start: 0.8085 (tp40) cc_final: 0.7602 (tp40) REVERT: L 151 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8959 (mmmt) REVERT: L 185 LYS cc_start: 0.8640 (tppp) cc_final: 0.8191 (tptt) REVERT: A 58 ASP cc_start: 0.8861 (t0) cc_final: 0.8608 (t0) outliers start: 30 outliers final: 9 residues processed: 146 average time/residue: 0.4506 time to fit residues: 68.6038 Evaluate side-chains 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 139 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN A 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064734 restraints weight = 11826.951| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.83 r_work: 0.2798 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6425 Z= 0.135 Angle : 0.624 8.242 8760 Z= 0.311 Chirality : 0.045 0.135 968 Planarity : 0.004 0.042 1128 Dihedral : 4.439 22.758 868 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.48 % Allowed : 19.42 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.30), residues: 777 helix: 1.08 (0.58), residues: 71 sheet: 1.42 (0.29), residues: 299 loop : 0.60 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 41 TYR 0.010 0.001 TYR B 123 PHE 0.020 0.001 PHE L 120 TRP 0.010 0.001 TRP A 48 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 6418) covalent geometry : angle 0.62423 / 0.31 ( 8746) SS BOND : bond 0.00451 / 0.23 ( 7) SS BOND : angle 0.57850 / 0.31 ( 14) hydrogen bonds : bond 0.03473 / 2.35 ( 263) hydrogen bonds : angle 5.46443 / 3.79 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8441 (t0) cc_final: 0.7501 (t0) REVERT: H 76 LYS cc_start: 0.9544 (mtmp) cc_final: 0.8908 (mtmp) REVERT: H 208 ILE cc_start: 0.9104 (tp) cc_final: 0.8579 (pp) REVERT: H 212 ASN cc_start: 0.8259 (p0) cc_final: 0.8009 (p0) REVERT: L 17 GLU cc_start: 0.8417 (pt0) cc_final: 0.8190 (pt0) REVERT: L 82 GLU cc_start: 0.8709 (pp20) cc_final: 0.8275 (pp20) REVERT: L 83 ASP cc_start: 0.8470 (m-30) cc_final: 0.7872 (m-30) REVERT: L 109 LYS cc_start: 0.9110 (tppp) cc_final: 0.8888 (ttpp) REVERT: L 149 GLN cc_start: 0.8211 (tp40) cc_final: 0.7822 (tp40) REVERT: L 185 LYS cc_start: 0.8578 (tppp) cc_final: 0.8117 (tptt) REVERT: A 58 ASP cc_start: 0.8804 (t0) cc_final: 0.8560 (t0) outliers start: 24 outliers final: 8 residues processed: 142 average time/residue: 0.4915 time to fit residues: 72.8940 Evaluate side-chains 128 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 203 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 184 GLN L 90 GLN L 139 ASN L 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.099846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065972 restraints weight = 11831.486| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.85 r_work: 0.2821 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6425 Z= 0.118 Angle : 0.621 7.941 8760 Z= 0.306 Chirality : 0.044 0.137 968 Planarity : 0.004 0.042 1128 Dihedral : 4.268 20.745 868 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.19 % Allowed : 20.72 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.31), residues: 777 helix: 1.16 (0.61), residues: 71 sheet: 1.41 (0.29), residues: 300 loop : 0.71 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 41 TYR 0.009 0.001 TYR B 123 PHE 0.022 0.001 PHE L 120 TRP 0.008 0.001 TRP H 52 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6418) covalent geometry : angle 0.62113 / 0.31 ( 8746) SS BOND : bond 0.00297 / 0.16 ( 7) SS BOND : angle 0.65290 / 0.36 ( 14) hydrogen bonds : bond 0.03120 / 2.10 ( 263) hydrogen bonds : angle 5.12761 / 3.55 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8434 (t0) cc_final: 0.8022 (t0) REVERT: H 212 ASN cc_start: 0.8156 (p0) cc_final: 0.7897 (p0) REVERT: L 24 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: L 109 LYS cc_start: 0.9091 (tppp) cc_final: 0.8880 (ttpp) REVERT: L 149 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7726 (tp40) REVERT: L 169 ASP cc_start: 0.8498 (t0) cc_final: 0.8236 (t0) REVERT: L 185 LYS cc_start: 0.8594 (tppp) cc_final: 0.8231 (tptt) REVERT: B 65 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8693 (tttm) REVERT: B 148 ILE cc_start: 0.9173 (mt) cc_final: 0.8945 (mm) REVERT: A 30 ASP cc_start: 0.9135 (m-30) cc_final: 0.8775 (m-30) REVERT: A 58 ASP cc_start: 0.8797 (t0) cc_final: 0.8543 (t0) REVERT: A 129 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8723 (mm-40) REVERT: A 163 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8261 (tp) outliers start: 22 outliers final: 7 residues processed: 139 average time/residue: 0.4679 time to fit residues: 68.1129 Evaluate side-chains 126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 184 GLN L 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.096887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062495 restraints weight = 12140.335| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.88 r_work: 0.2741 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6425 Z= 0.214 Angle : 0.662 7.671 8760 Z= 0.328 Chirality : 0.045 0.142 968 Planarity : 0.004 0.042 1128 Dihedral : 4.457 17.276 868 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.91 % Allowed : 20.87 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.31), residues: 777 helix: 1.05 (0.60), residues: 71 sheet: 1.18 (0.28), residues: 316 loop : 0.71 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 41 TYR 0.026 0.001 TYR B 60 PHE 0.021 0.002 PHE L 120 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 ( 6418) covalent geometry : angle 0.66194 / 0.33 ( 8746) SS BOND : bond 0.00277 / 0.15 ( 7) SS BOND : angle 0.68429 / 0.37 ( 14) hydrogen bonds : bond 0.03469 / 2.34 ( 263) hydrogen bonds : angle 5.33804 / 3.70 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8506 (t0) cc_final: 0.7670 (t0) REVERT: H 76 LYS cc_start: 0.9567 (mtmp) cc_final: 0.8847 (mtmp) REVERT: H 212 ASN cc_start: 0.8198 (p0) cc_final: 0.7995 (p0) REVERT: H 222 LYS cc_start: 0.8479 (tppt) cc_final: 0.8170 (tppp) REVERT: L 109 LYS cc_start: 0.9117 (tppp) cc_final: 0.8909 (ttpp) REVERT: L 185 LYS cc_start: 0.8667 (tppp) cc_final: 0.8286 (tptt) REVERT: A 58 ASP cc_start: 0.8846 (t0) cc_final: 0.8558 (t0) REVERT: A 63 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9119 (mm) outliers start: 27 outliers final: 10 residues processed: 140 average time/residue: 0.4743 time to fit residues: 69.2550 Evaluate side-chains 137 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 139 ASN A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.062550 restraints weight = 11936.917| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.84 r_work: 0.2750 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6425 Z= 0.212 Angle : 0.682 8.061 8760 Z= 0.336 Chirality : 0.046 0.143 968 Planarity : 0.004 0.045 1128 Dihedral : 4.501 16.685 868 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.32 % Allowed : 23.48 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.30), residues: 777 helix: 1.04 (0.60), residues: 71 sheet: 1.08 (0.28), residues: 318 loop : 0.66 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 41 TYR 0.019 0.001 TYR B 60 PHE 0.024 0.002 PHE L 120 TRP 0.008 0.001 TRP A 48 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 6418) covalent geometry : angle 0.68108 / 0.34 ( 8746) SS BOND : bond 0.00244 / 0.14 ( 7) SS BOND : angle 0.91207 / 0.51 ( 14) hydrogen bonds : bond 0.03414 / 2.30 ( 263) hydrogen bonds : angle 5.29691 / 3.67 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8537 (t0) cc_final: 0.7717 (t0) REVERT: H 76 LYS cc_start: 0.9573 (mtmp) cc_final: 0.8843 (mtmp) REVERT: L 24 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8261 (ttm-80) REVERT: L 145 GLU cc_start: 0.8269 (pp20) cc_final: 0.7667 (pp20) REVERT: L 147 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8247 (mptt) REVERT: L 185 LYS cc_start: 0.8671 (tppp) cc_final: 0.8276 (tptt) REVERT: A 58 ASP cc_start: 0.8857 (t0) cc_final: 0.8567 (t0) REVERT: A 63 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9155 (mm) REVERT: A 88 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8627 (mt-10) outliers start: 16 outliers final: 6 residues processed: 134 average time/residue: 0.4646 time to fit residues: 64.8960 Evaluate side-chains 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 139 ASN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.060642 restraints weight = 12072.450| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.83 r_work: 0.2699 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 6425 Z= 0.299 Angle : 0.727 10.068 8760 Z= 0.363 Chirality : 0.047 0.161 968 Planarity : 0.005 0.049 1128 Dihedral : 4.868 20.152 868 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 23.91 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 777 helix: 0.55 (0.58), residues: 77 sheet: 0.91 (0.27), residues: 324 loop : 0.63 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 41 TYR 0.018 0.002 TYR B 60 PHE 0.033 0.002 PHE H 135 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.30 ( 6418) covalent geometry : angle 0.72707 / 0.36 ( 8746) SS BOND : bond 0.00343 / 0.18 ( 7) SS BOND : angle 0.89631 / 0.49 ( 14) hydrogen bonds : bond 0.03750 / 2.55 ( 263) hydrogen bonds : angle 5.57860 / 3.82 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8564 (t0) cc_final: 0.8067 (t0) REVERT: H 212 ASN cc_start: 0.8209 (p0) cc_final: 0.7947 (p0) REVERT: H 214 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8836 (mmpt) REVERT: L 145 GLU cc_start: 0.8079 (pp20) cc_final: 0.7582 (pp20) REVERT: L 196 CYS cc_start: 0.6463 (p) cc_final: 0.5886 (p) REVERT: L 197 GLU cc_start: 0.8612 (tp30) cc_final: 0.8164 (tp30) REVERT: A 58 ASP cc_start: 0.8901 (t0) cc_final: 0.8604 (t0) REVERT: A 63 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9115 (mm) outliers start: 16 outliers final: 7 residues processed: 131 average time/residue: 0.4298 time to fit residues: 58.8464 Evaluate side-chains 126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 139 ASN A 127 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065141 restraints weight = 12106.378| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.90 r_work: 0.2793 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6425 Z= 0.127 Angle : 0.683 9.458 8760 Z= 0.334 Chirality : 0.045 0.151 968 Planarity : 0.004 0.054 1128 Dihedral : 4.476 16.254 868 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.88 % Allowed : 24.78 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.30), residues: 777 helix: 1.07 (0.61), residues: 71 sheet: 1.16 (0.28), residues: 310 loop : 0.54 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 41 TYR 0.016 0.001 TYR B 60 PHE 0.024 0.002 PHE L 118 TRP 0.012 0.001 TRP A 48 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 6418) covalent geometry : angle 0.68311 / 0.33 ( 8746) SS BOND : bond 0.00208 / 0.12 ( 7) SS BOND : angle 0.69456 / 0.38 ( 14) hydrogen bonds : bond 0.03188 / 2.15 ( 263) hydrogen bonds : angle 5.10431 / 3.52 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8526 (t0) cc_final: 0.7944 (t0) REVERT: H 76 LYS cc_start: 0.9559 (mtmp) cc_final: 0.9187 (mtmp) REVERT: H 212 ASN cc_start: 0.8203 (p0) cc_final: 0.7890 (p0) REVERT: H 214 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8756 (mmpt) REVERT: L 185 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8156 (mptt) REVERT: L 196 CYS cc_start: 0.6342 (p) cc_final: 0.5703 (p) REVERT: B 53 GLN cc_start: 0.9419 (mp10) cc_final: 0.9104 (mp10) REVERT: B 69 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8487 (mm-30) REVERT: B 128 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8827 (mmmm) REVERT: B 148 ILE cc_start: 0.9186 (mt) cc_final: 0.8888 (mm) REVERT: A 30 ASP cc_start: 0.9103 (m-30) cc_final: 0.8744 (m-30) REVERT: A 58 ASP cc_start: 0.8829 (t0) cc_final: 0.8567 (t0) REVERT: A 88 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8641 (mt-10) REVERT: A 163 ILE cc_start: 0.8686 (mm) cc_final: 0.8386 (tp) outliers start: 13 outliers final: 4 residues processed: 143 average time/residue: 0.4580 time to fit residues: 68.3496 Evaluate side-chains 130 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 177 HIS L 139 ASN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064363 restraints weight = 11989.884| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.86 r_work: 0.2784 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6425 Z= 0.150 Angle : 0.701 10.523 8760 Z= 0.341 Chirality : 0.046 0.163 968 Planarity : 0.005 0.057 1128 Dihedral : 4.486 15.933 868 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.16 % Allowed : 26.52 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.30), residues: 777 helix: 1.17 (0.59), residues: 71 sheet: 1.06 (0.28), residues: 318 loop : 0.66 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 41 TYR 0.016 0.001 TYR A 153 PHE 0.025 0.002 PHE H 135 TRP 0.009 0.001 TRP A 48 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6418) covalent geometry : angle 0.70071 / 0.34 ( 8746) SS BOND : bond 0.00188 / 0.11 ( 7) SS BOND : angle 0.80309 / 0.44 ( 14) hydrogen bonds : bond 0.03173 / 2.14 ( 263) hydrogen bonds : angle 5.13364 / 3.55 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8520 (t0) cc_final: 0.7920 (t0) REVERT: H 76 LYS cc_start: 0.9560 (mtmp) cc_final: 0.9179 (mtmp) REVERT: H 212 ASN cc_start: 0.8169 (p0) cc_final: 0.7874 (p0) REVERT: H 214 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8789 (mmpt) REVERT: L 149 GLN cc_start: 0.7931 (tp40) cc_final: 0.7423 (tp40) REVERT: L 185 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8170 (mptt) REVERT: L 196 CYS cc_start: 0.6408 (p) cc_final: 0.5802 (p) REVERT: B 53 GLN cc_start: 0.9440 (mp10) cc_final: 0.9080 (mp10) REVERT: B 69 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8493 (mm-30) REVERT: B 128 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8802 (mmmm) REVERT: A 30 ASP cc_start: 0.9126 (m-30) cc_final: 0.8745 (m-30) REVERT: A 58 ASP cc_start: 0.8949 (t0) cc_final: 0.8679 (t0) REVERT: A 88 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8638 (mt-10) REVERT: A 163 ILE cc_start: 0.8693 (mm) cc_final: 0.8410 (tp) outliers start: 8 outliers final: 7 residues processed: 135 average time/residue: 0.4973 time to fit residues: 69.9936 Evaluate side-chains 131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 179 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 118 GLN L 139 ASN B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.062688 restraints weight = 12023.068| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.86 r_work: 0.2751 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6425 Z= 0.211 Angle : 0.736 11.179 8760 Z= 0.358 Chirality : 0.047 0.162 968 Planarity : 0.005 0.060 1128 Dihedral : 4.611 16.550 868 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 26.52 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.30), residues: 777 helix: 0.80 (0.58), residues: 77 sheet: 1.05 (0.28), residues: 312 loop : 0.58 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 41 TYR 0.013 0.002 TYR L 188 PHE 0.026 0.002 PHE H 135 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 6418) covalent geometry : angle 0.73577 / 0.36 ( 8746) SS BOND : bond 0.00217 / 0.12 ( 7) SS BOND : angle 0.94957 / 0.53 ( 14) hydrogen bonds : bond 0.03378 / 2.28 ( 263) hydrogen bonds : angle 5.28095 / 3.65 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.8529 (t0) cc_final: 0.8046 (t0) REVERT: H 212 ASN cc_start: 0.8180 (p0) cc_final: 0.7899 (p0) REVERT: L 24 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.7988 (tpp-160) REVERT: L 71 ASP cc_start: 0.8733 (m-30) cc_final: 0.8392 (t70) REVERT: L 185 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8161 (mptt) REVERT: L 196 CYS cc_start: 0.6380 (p) cc_final: 0.5768 (p) REVERT: B 64 GLN cc_start: 0.8925 (mt0) cc_final: 0.8670 (mt0) REVERT: B 128 LYS cc_start: 0.9281 (mmmt) cc_final: 0.8792 (mmmm) REVERT: A 58 ASP cc_start: 0.8948 (t0) cc_final: 0.8674 (t0) REVERT: A 88 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8587 (mt-10) outliers start: 8 outliers final: 7 residues processed: 129 average time/residue: 0.4734 time to fit residues: 63.6641 Evaluate side-chains 131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 118 GLN L 139 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062739 restraints weight = 12129.428| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.85 r_work: 0.2750 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6425 Z= 0.208 Angle : 0.735 10.931 8760 Z= 0.358 Chirality : 0.047 0.169 968 Planarity : 0.005 0.060 1128 Dihedral : 4.642 16.664 868 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 26.23 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.30), residues: 777 helix: 0.83 (0.58), residues: 77 sheet: 1.00 (0.28), residues: 312 loop : 0.56 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 41 TYR 0.013 0.001 TYR B 123 PHE 0.023 0.002 PHE L 118 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 ( 6418) covalent geometry : angle 0.73434 / 0.36 ( 8746) SS BOND : bond 0.00203 / 0.12 ( 7) SS BOND : angle 0.88232 / 0.49 ( 14) hydrogen bonds : bond 0.03376 / 2.28 ( 263) hydrogen bonds : angle 5.29195 / 3.66 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2409.86 seconds wall clock time: 41 minutes 40.18 seconds (2500.18 seconds total)