Starting phenix.real_space_refine on Wed Jan 17 22:37:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1b_27121/01_2024/8d1b_27121.pdb" } resolution = 3.57 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= 0.041 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 38 5.16 5 C 4196 2.51 5 N 1204 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 861": "NH1" <-> "NH2" Residue "D ARG 867": "NH1" <-> "NH2" Residue "D PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 924": "NH1" <-> "NH2" Residue "D ARG 927": "NH1" <-> "NH2" Residue "D ASP 933": "OD1" <-> "OD2" Residue "D ASP 942": "OD1" <-> "OD2" Residue "D TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 971": "OE1" <-> "OE2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ARG 867": "NH1" <-> "NH2" Residue "C PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 924": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ASP 933": "OD1" <-> "OD2" Residue "C ASP 942": "OD1" <-> "OD2" Residue "C TYR 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 971": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ASP 117": "OD1" <-> "OD2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6724 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1379 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "C" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1379 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "B" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1983 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Chain: "A" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1983 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain breaks: 1 Time building chain proxies: 4.11, per 1000 atoms: 0.61 Number of scatterers: 6724 At special positions: 0 Unit cell: (86.355, 88.065, 112.005, 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 38 16.00 O 1286 8.00 N 1204 7.00 C 4196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 987 " - pdb=" SG CYS D1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 317 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 10.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'D' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL D 857 " --> pdb=" O ILE D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR D 995 " --> pdb=" O THR D 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 removed outlier: 4.190A pdb=" N VAL C 857 " --> pdb=" O ILE C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 996 removed outlier: 3.983A pdb=" N THR C 995 " --> pdb=" O THR C 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 removed outlier: 3.788A pdb=" N ALA B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 3.660A pdb=" N GLN B 96 " --> pdb=" O PRO B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.787A pdb=" N ALA A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.659A pdb=" N GLN A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.720A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 136 through 140 Processing sheet with id=AA1, first strand: chain 'D' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY D 895 " --> pdb=" O VAL D 902 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 894 through 897 removed outlier: 3.562A pdb=" N GLY C 895 " --> pdb=" O VAL C 902 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.590A pdb=" N ASP B 271 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 146 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 149 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR B 173 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 219 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 216 through 221 removed outlier: 3.671A pdb=" N GLY B 219 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 173 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 149 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG A 146 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP A 271 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.718A pdb=" N GLN B 237 " --> pdb=" O ARG B 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 3.717A pdb=" N GLN A 237 " --> pdb=" O ARG A 240 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 162 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: 1.50 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2301 1.34 - 1.46: 1523 1.46 - 1.58: 2976 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6858 Sorted by residual: bond pdb=" C GLN A 114 " pdb=" N ALA A 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.10e+00 bond pdb=" C GLN B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 1.331 1.306 0.025 1.73e-02 3.34e+03 2.02e+00 bond pdb=" C ALA B 106 " pdb=" N ASN B 107 " ideal model delta sigma weight residual 1.331 1.311 0.019 1.38e-02 5.25e+03 1.97e+00 bond pdb=" C ALA A 106 " pdb=" N ASN A 107 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.38e-02 5.25e+03 1.68e+00 bond pdb=" CB VAL A 134 " pdb=" CG1 VAL A 134 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.63e+00 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.87: 182 105.87 - 112.91: 3515 112.91 - 119.94: 2348 119.94 - 126.98: 3171 126.98 - 134.01: 78 Bond angle restraints: 9294 Sorted by residual: angle pdb=" N GLY B 86 " pdb=" CA GLY B 86 " pdb=" C GLY B 86 " ideal model delta sigma weight residual 113.99 108.54 5.45 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N GLY A 86 " pdb=" CA GLY A 86 " pdb=" C GLY A 86 " ideal model delta sigma weight residual 113.99 108.55 5.44 1.28e+00 6.10e-01 1.81e+01 angle pdb=" N LYS B 257 " pdb=" CA LYS B 257 " pdb=" C LYS B 257 " ideal model delta sigma weight residual 109.83 104.83 5.00 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N LYS A 257 " pdb=" CA LYS A 257 " pdb=" C LYS A 257 " ideal model delta sigma weight residual 109.83 104.88 4.95 1.27e+00 6.20e-01 1.52e+01 angle pdb=" CA LEU B 71 " pdb=" C LEU B 71 " pdb=" N SER B 72 " ideal model delta sigma weight residual 114.17 119.36 -5.19 1.45e+00 4.76e-01 1.28e+01 ... (remaining 9289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3664 17.78 - 35.56: 390 35.56 - 53.34: 64 53.34 - 71.13: 6 71.13 - 88.91: 4 Dihedral angle restraints: 4128 sinusoidal: 1656 harmonic: 2472 Sorted by residual: dihedral pdb=" CA ARG C 886 " pdb=" C ARG C 886 " pdb=" N PRO C 887 " pdb=" CA PRO C 887 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG D 886 " pdb=" C ARG D 886 " pdb=" N PRO D 887 " pdb=" CA PRO D 887 " ideal model delta harmonic sigma weight residual 180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLU A 263 " pdb=" C GLU A 263 " pdb=" N VAL A 264 " pdb=" CA VAL A 264 " ideal model delta harmonic sigma weight residual 180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 550 0.037 - 0.073: 308 0.073 - 0.109: 119 0.109 - 0.146: 23 0.146 - 0.182: 10 Chirality restraints: 1010 Sorted by residual: chirality pdb=" CA PRO D 887 " pdb=" N PRO D 887 " pdb=" C PRO D 887 " pdb=" CB PRO D 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CA PRO C 887 " pdb=" N PRO C 887 " pdb=" C PRO C 887 " pdb=" CB PRO C 887 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB THR B 173 " pdb=" CA THR B 173 " pdb=" OG1 THR B 173 " pdb=" CG2 THR B 173 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1007 not shown) Planarity restraints: 1232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 92 " -0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 93 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 92 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO B 93 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 257 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO B 258 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.039 5.00e-02 4.00e+02 ... (remaining 1229 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 168 2.65 - 3.21: 6399 3.21 - 3.77: 9281 3.77 - 4.34: 12952 4.34 - 4.90: 21299 Nonbonded interactions: 50099 Sorted by model distance: nonbonded pdb=" OE1 GLN B 73 " pdb=" NH2 ARG B 240 " model vdw 2.084 2.520 nonbonded pdb=" OE1 GLN A 73 " pdb=" NH2 ARG A 240 " model vdw 2.085 2.520 nonbonded pdb=" NZ LYS C 950 " pdb=" OD1 ASP A 259 " model vdw 2.105 2.520 nonbonded pdb=" O SER B 261 " pdb=" OG SER B 261 " model vdw 2.112 2.440 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.112 2.440 ... (remaining 50094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.320 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: 22.050 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6858 Z= 0.405 Angle : 1.086 9.237 9294 Z= 0.620 Chirality : 0.052 0.182 1010 Planarity : 0.008 0.084 1232 Dihedral : 14.425 88.908 2532 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.13 % Favored : 75.87 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.32 (0.22), residues: 862 helix: -5.21 (0.17), residues: 100 sheet: -3.30 (0.35), residues: 164 loop : -4.63 (0.20), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 182 HIS 0.003 0.001 HIS D 926 PHE 0.013 0.002 PHE D 868 TYR 0.023 0.002 TYR A 62 ARG 0.005 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.816 Fit side-chains REVERT: D 965 TYR cc_start: 0.8098 (m-80) cc_final: 0.7772 (m-80) REVERT: D 998 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6789 (m90) REVERT: D 1010 ASN cc_start: 0.8319 (t0) cc_final: 0.8105 (t0) REVERT: C 965 TYR cc_start: 0.8096 (m-80) cc_final: 0.7685 (m-80) REVERT: C 998 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6721 (m90) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.1474 time to fit residues: 27.0080 Evaluate side-chains 102 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 998 HIS Chi-restraints excluded: chain C residue 998 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS B 161 GLN B 165 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 GLN A 165 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6858 Z= 0.236 Angle : 0.808 8.494 9294 Z= 0.409 Chirality : 0.047 0.193 1010 Planarity : 0.006 0.066 1232 Dihedral : 6.981 26.893 962 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.19 % Favored : 79.81 % Rotamer: Outliers : 1.39 % Allowed : 9.70 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.80 (0.23), residues: 862 helix: -4.71 (0.27), residues: 90 sheet: -2.77 (0.39), residues: 160 loop : -4.37 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.006 0.001 HIS D 990 PHE 0.008 0.001 PHE C 865 TYR 0.021 0.002 TYR A 62 ARG 0.003 0.000 ARG D 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.801 Fit side-chains REVERT: D 905 TYR cc_start: 0.8881 (p90) cc_final: 0.8629 (p90) REVERT: D 955 MET cc_start: 0.6215 (ptt) cc_final: 0.5984 (ptt) REVERT: D 965 TYR cc_start: 0.7963 (m-80) cc_final: 0.7618 (m-80) REVERT: D 1010 ASN cc_start: 0.8244 (t0) cc_final: 0.7986 (t0) REVERT: C 965 TYR cc_start: 0.7999 (m-80) cc_final: 0.7721 (m-80) REVERT: C 975 HIS cc_start: 0.6398 (m-70) cc_final: 0.6191 (m170) REVERT: C 1010 ASN cc_start: 0.8524 (t0) cc_final: 0.8288 (t0) outliers start: 10 outliers final: 3 residues processed: 121 average time/residue: 0.1493 time to fit residues: 25.7924 Evaluate side-chains 105 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 990 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.0000 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 839 GLN D 990 HIS C 990 HIS B 237 GLN A 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.004 0.048 6858 Z= 0.238 Angle : 0.779 7.719 9294 Z= 0.393 Chirality : 0.046 0.191 1010 Planarity : 0.006 0.064 1232 Dihedral : 6.589 27.777 958 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.26 % Favored : 80.74 % Rotamer: Outliers : 0.83 % Allowed : 15.65 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.23), residues: 862 helix: -4.39 (0.31), residues: 90 sheet: -2.72 (0.37), residues: 164 loop : -4.34 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.004 0.001 HIS D 990 PHE 0.007 0.001 PHE D 868 TYR 0.015 0.001 TYR B 80 ARG 0.003 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.895 Fit side-chains REVERT: D 839 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6373 (mt0) REVERT: D 905 TYR cc_start: 0.8862 (p90) cc_final: 0.8584 (p90) REVERT: D 911 VAL cc_start: 0.9161 (t) cc_final: 0.8901 (p) REVERT: D 1010 ASN cc_start: 0.8144 (t0) cc_final: 0.7761 (t0) REVERT: C 1010 ASN cc_start: 0.8367 (t0) cc_final: 0.7872 (t0) outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1522 time to fit residues: 23.9241 Evaluate side-chains 108 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 839 GLN Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.4980 chunk 57 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.0070 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS C 990 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6858 Z= 0.199 Angle : 0.739 8.384 9294 Z= 0.366 Chirality : 0.044 0.189 1010 Planarity : 0.005 0.063 1232 Dihedral : 6.166 27.761 958 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.82 % Favored : 83.18 % Rotamer: Outliers : 2.35 % Allowed : 16.62 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.23), residues: 862 helix: -4.29 (0.32), residues: 88 sheet: -2.50 (0.37), residues: 164 loop : -4.17 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 288 HIS 0.002 0.000 HIS C 990 PHE 0.008 0.001 PHE D 840 TYR 0.009 0.001 TYR A 80 ARG 0.003 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.736 Fit side-chains REVERT: D 905 TYR cc_start: 0.8850 (p90) cc_final: 0.8615 (p90) REVERT: D 1010 ASN cc_start: 0.8169 (t0) cc_final: 0.7576 (t0) REVERT: C 1010 ASN cc_start: 0.8328 (t0) cc_final: 0.7793 (t0) REVERT: B 88 MET cc_start: 0.5942 (mmp) cc_final: 0.5675 (mmm) REVERT: A 88 MET cc_start: 0.5913 (mmp) cc_final: 0.5668 (mmm) outliers start: 17 outliers final: 5 residues processed: 119 average time/residue: 0.1541 time to fit residues: 26.2999 Evaluate side-chains 103 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6858 Z= 0.294 Angle : 0.791 8.819 9294 Z= 0.391 Chirality : 0.046 0.191 1010 Planarity : 0.006 0.063 1232 Dihedral : 6.153 27.392 958 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.95 % Favored : 80.05 % Rotamer: Outliers : 1.80 % Allowed : 19.39 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.24), residues: 862 helix: -4.33 (0.30), residues: 96 sheet: -2.36 (0.38), residues: 164 loop : -4.15 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.008 0.001 HIS D 990 PHE 0.008 0.002 PHE D 868 TYR 0.010 0.001 TYR D 905 ARG 0.004 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.800 Fit side-chains REVERT: D 905 TYR cc_start: 0.8878 (p90) cc_final: 0.8667 (p90) REVERT: D 1010 ASN cc_start: 0.8243 (t0) cc_final: 0.7937 (t0) REVERT: C 1010 ASN cc_start: 0.8250 (t0) cc_final: 0.7680 (t0) outliers start: 13 outliers final: 7 residues processed: 109 average time/residue: 0.1484 time to fit residues: 23.3526 Evaluate side-chains 101 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 989 SER Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 37 optimal weight: 0.0060 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 overall best weight: 0.0818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 990 HIS D1012 ASN C 990 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6858 Z= 0.183 Angle : 0.728 10.166 9294 Z= 0.359 Chirality : 0.044 0.183 1010 Planarity : 0.005 0.061 1232 Dihedral : 5.837 27.212 958 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.47 % Favored : 83.53 % Rotamer: Outliers : 1.66 % Allowed : 19.81 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.24), residues: 862 helix: -3.99 (0.35), residues: 96 sheet: -2.16 (0.39), residues: 164 loop : -4.02 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 245 HIS 0.010 0.001 HIS D 990 PHE 0.010 0.001 PHE C 991 TYR 0.010 0.001 TYR A 80 ARG 0.002 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.811 Fit side-chains REVERT: C 1010 ASN cc_start: 0.8200 (t0) cc_final: 0.7650 (t0) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.1546 time to fit residues: 25.2559 Evaluate side-chains 108 residues out of total 722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 892 ILE Chi-restraints excluded: chain D residue 989 SER Chi-restraints excluded: chain D residue 990 HIS Chi-restraints excluded: chain C residue 892 ILE Chi-restraints excluded: chain C residue 989 SER Chi-restraints excluded: chain C residue 990 HIS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain A residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9281 > 50: distance: 88 - 92: 11.925 distance: 92 - 93: 15.207 distance: 93 - 94: 28.119 distance: 93 - 96: 24.425 distance: 94 - 95: 39.959 distance: 94 - 97: 21.140 distance: 97 - 98: 22.969 distance: 98 - 99: 20.526 distance: 98 - 101: 22.879 distance: 99 - 100: 23.457 distance: 99 - 104: 27.228 distance: 101 - 102: 15.161 distance: 101 - 103: 34.614 distance: 104 - 105: 7.288 distance: 105 - 106: 11.520 distance: 105 - 108: 24.095 distance: 106 - 107: 19.350 distance: 106 - 115: 23.988 distance: 108 - 109: 16.980 distance: 109 - 110: 16.319 distance: 109 - 111: 7.498 distance: 110 - 112: 21.164 distance: 111 - 113: 7.749 distance: 112 - 114: 13.275 distance: 113 - 114: 13.962 distance: 115 - 116: 10.784 distance: 116 - 117: 36.797 distance: 116 - 119: 17.902 distance: 117 - 118: 34.779 distance: 117 - 127: 53.740 distance: 119 - 120: 20.101 distance: 120 - 121: 28.060 distance: 120 - 122: 25.406 distance: 121 - 123: 17.481 distance: 122 - 124: 13.707 distance: 123 - 125: 6.650 distance: 124 - 125: 14.050 distance: 125 - 126: 24.374 distance: 127 - 128: 18.993 distance: 128 - 129: 24.885 distance: 129 - 130: 33.480 distance: 129 - 131: 15.003 distance: 131 - 132: 5.946 distance: 132 - 133: 50.330 distance: 132 - 135: 47.422 distance: 133 - 134: 29.484 distance: 133 - 139: 26.362 distance: 135 - 136: 44.996 distance: 136 - 137: 16.439 distance: 136 - 138: 26.040 distance: 139 - 140: 26.184 distance: 140 - 141: 6.202 distance: 140 - 143: 22.393 distance: 141 - 142: 19.866 distance: 141 - 148: 17.650 distance: 143 - 144: 31.033 distance: 144 - 145: 16.556 distance: 145 - 146: 8.621 distance: 146 - 147: 10.010 distance: 148 - 149: 13.623 distance: 148 - 154: 14.960 distance: 149 - 150: 12.284 distance: 149 - 152: 8.117 distance: 150 - 151: 26.429 distance: 150 - 155: 19.935 distance: 152 - 153: 17.849 distance: 153 - 154: 14.488 distance: 155 - 156: 13.925 distance: 156 - 157: 37.974 distance: 156 - 159: 26.896 distance: 157 - 158: 48.343 distance: 157 - 163: 46.498 distance: 159 - 160: 18.800 distance: 160 - 161: 28.501 distance: 160 - 162: 16.781 distance: 163 - 164: 22.299 distance: 164 - 165: 16.242 distance: 164 - 167: 12.276 distance: 165 - 166: 26.288 distance: 165 - 171: 8.035 distance: 167 - 168: 29.531 distance: 168 - 169: 23.468 distance: 168 - 170: 32.572