Starting phenix.real_space_refine on Tue May 7 06:53:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h87_34531/05_2024/8h87_34531_updated.pdb" } resolution = 2.53 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= 0.009 sd= 0.430 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 48 5.16 5 C 4830 2.51 5 N 978 2.21 5 O 1224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 7083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "A" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "B" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2097 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 264 Unusual residues: {'PLM': 9, 'PSC': 6, 'RET': 1} Classifications: {'undetermined': 16, 'water': 49} Link IDs: {None: 64} Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-1': 4, 'PSC:plan-2': 4, 'PSC:plan-3': 4, 'PSC:plan-4': 4, 'PLM:plan-1': 8} Unresolved non-hydrogen planarities: 84 Time building chain proxies: 4.39, per 1000 atoms: 0.62 Number of scatterers: 7083 At special positions: 0 Unit cell: (78.02, 77.19, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 3 15.00 O 1224 8.00 N 978 7.00 C 4830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 69.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 removed outlier: 3.669A pdb=" N LEU A 49 " --> pdb=" O TYR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 89 removed outlier: 4.062A pdb=" N SER A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 121 removed outlier: 3.840A pdb=" N PHE A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N CYS A 110 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 126 through 145 Processing helix chain 'A' and resid 149 through 179 removed outlier: 3.602A pdb=" N PHE A 162 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE A 163 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.558A pdb=" N ILE A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 207 removed outlier: 3.521A pdb=" N TRP A 190 " --> pdb=" O ARG A 186 " (cutoff:3.500A) Proline residue: A 200 - end of helix Proline residue: A 203 - end of helix removed outlier: 3.986A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'B' and resid 22 through 49 removed outlier: 3.669A pdb=" N LEU B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 89 removed outlier: 4.062A pdb=" N SER B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 78 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 121 removed outlier: 3.840A pdb=" N PHE B 108 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N CYS B 110 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 126 through 145 Processing helix chain 'B' and resid 149 through 179 removed outlier: 3.602A pdb=" N PHE B 162 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 163 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.558A pdb=" N ILE B 170 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 177 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN B 178 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 207 removed outlier: 3.521A pdb=" N TRP B 190 " --> pdb=" O ARG B 186 " (cutoff:3.500A) Proline residue: B 200 - end of helix Proline residue: B 203 - end of helix removed outlier: 3.986A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 234 through 251 Processing helix chain 'C' and resid 22 through 49 removed outlier: 3.669A pdb=" N LEU C 49 " --> pdb=" O TYR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 89 removed outlier: 4.062A pdb=" N SER C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 78 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 121 removed outlier: 3.840A pdb=" N PHE C 108 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N CYS C 110 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 126 through 145 Processing helix chain 'C' and resid 149 through 179 removed outlier: 3.602A pdb=" N PHE C 162 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE C 163 " --> pdb=" O CYS C 160 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.558A pdb=" N ILE C 170 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 177 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN C 178 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 207 removed outlier: 3.521A pdb=" N TRP C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Proline residue: C 200 - end of helix Proline residue: C 203 - end of helix removed outlier: 3.986A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 232 Processing helix chain 'C' and resid 234 through 251 384 hydrogen bonds defined for protein. 702 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: 1.62 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1169 1.33 - 1.46: 2603 1.46 - 1.59: 3287 1.59 - 1.72: 6 1.72 - 1.85: 63 Bond restraints: 7128 Sorted by residual: bond pdb=" C6 PSC A 404 " pdb=" C7 PSC A 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC C 404 " pdb=" C7 PSC C 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C6 PSC B 404 " pdb=" C7 PSC B 404 " ideal model delta sigma weight residual 1.523 1.314 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA SER B 217 " pdb=" CB SER B 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.75e+01 bond pdb=" CA SER A 217 " pdb=" CB SER A 217 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.61e-02 3.86e+03 1.75e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.69: 227 105.69 - 112.80: 3128 112.80 - 119.92: 2966 119.92 - 127.04: 3060 127.04 - 134.16: 120 Bond angle restraints: 9501 Sorted by residual: angle pdb=" C01 PSC B 402 " pdb=" C02 PSC B 402 " pdb=" O01 PSC B 402 " ideal model delta sigma weight residual 107.00 127.41 -20.41 3.00e+00 1.11e-01 4.63e+01 angle pdb=" C01 PSC C 402 " pdb=" C02 PSC C 402 " pdb=" O01 PSC C 402 " ideal model delta sigma weight residual 107.00 127.40 -20.40 3.00e+00 1.11e-01 4.62e+01 angle pdb=" C01 PSC A 402 " pdb=" C02 PSC A 402 " pdb=" O01 PSC A 402 " ideal model delta sigma weight residual 107.00 127.39 -20.39 3.00e+00 1.11e-01 4.62e+01 angle pdb=" N PRO C 182 " pdb=" CA PRO C 182 " pdb=" C PRO C 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.67e+01 angle pdb=" N PRO A 182 " pdb=" CA PRO A 182 " pdb=" C PRO A 182 " ideal model delta sigma weight residual 113.75 121.44 -7.69 1.49e+00 4.50e-01 2.66e+01 ... (remaining 9496 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 3900 32.13 - 64.27: 213 64.27 - 96.40: 12 96.40 - 128.53: 3 128.53 - 160.67: 3 Dihedral angle restraints: 4131 sinusoidal: 1869 harmonic: 2262 Sorted by residual: dihedral pdb=" N PSC A 402 " pdb=" C04 PSC A 402 " pdb=" C05 PSC A 402 " pdb=" O12 PSC A 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.22 -160.67 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC B 402 " pdb=" C04 PSC B 402 " pdb=" C05 PSC B 402 " pdb=" O12 PSC B 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.21 -160.66 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" N PSC C 402 " pdb=" C04 PSC C 402 " pdb=" C05 PSC C 402 " pdb=" O12 PSC C 402 " ideal model delta sinusoidal sigma weight residual -70.45 90.20 -160.65 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 4128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 460 0.049 - 0.098: 261 0.098 - 0.147: 139 0.147 - 0.196: 43 0.196 - 0.245: 24 Chirality restraints: 927 Sorted by residual: chirality pdb=" CB VAL B 17 " pdb=" CA VAL B 17 " pdb=" CG1 VAL B 17 " pdb=" CG2 VAL B 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB VAL C 17 " pdb=" CA VAL C 17 " pdb=" CG1 VAL C 17 " pdb=" CG2 VAL C 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB VAL A 17 " pdb=" CA VAL A 17 " pdb=" CG1 VAL A 17 " pdb=" CG2 VAL A 17 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 924 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PSC A 402 " -0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC A 402 " 0.088 2.00e-02 2.50e+03 pdb=" C8 PSC A 402 " -0.089 2.00e-02 2.50e+03 pdb=" C9 PSC A 402 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC C 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.43e+02 pdb=" C11 PSC C 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC C 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC C 402 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 PSC B 402 " 0.246 2.00e-02 2.50e+03 1.85e-01 3.42e+02 pdb=" C11 PSC B 402 " -0.088 2.00e-02 2.50e+03 pdb=" C8 PSC B 402 " 0.089 2.00e-02 2.50e+03 pdb=" C9 PSC B 402 " -0.247 2.00e-02 2.50e+03 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2129 2.82 - 3.34: 6697 3.34 - 3.86: 12671 3.86 - 4.38: 16564 4.38 - 4.90: 25055 Nonbonded interactions: 63116 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O HOH A 501 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR C 180 " pdb=" O HOH C 501 " model vdw 2.301 2.440 nonbonded pdb=" OH TYR B 180 " pdb=" O HOH B 501 " model vdw 2.301 2.440 nonbonded pdb=" N GLY A 52 " pdb=" OE1 GLU A 248 " model vdw 2.333 2.520 nonbonded pdb=" N GLY B 52 " pdb=" OE1 GLU B 248 " model vdw 2.333 2.520 ... (remaining 63111 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' selection = chain 'C' } 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: 0.300 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: 1.530 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.040 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.011 0.209 7128 Z= 0.684 Angle : 1.547 20.406 9501 Z= 0.941 Chirality : 0.080 0.245 927 Planarity : 0.017 0.185 1137 Dihedral : 18.835 160.666 2691 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.91 % Allowed : 1.82 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 771 helix: -1.08 (0.18), residues: 516 sheet: None (None), residues: 0 loop : 0.02 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.011 TRP C 42 HIS 0.012 0.006 HIS C 225 PHE 0.050 0.010 PHE A 150 TYR 0.043 0.010 TYR A 101 ARG 0.018 0.002 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASP cc_start: 0.8294 (m-30) cc_final: 0.7947 (m-30) REVERT: A 171 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6401 (ttp-170) REVERT: A 174 LYS cc_start: 0.7676 (mtpm) cc_final: 0.7077 (mtmt) REVERT: A 186 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7023 (ttm110) REVERT: A 204 LEU cc_start: 0.7840 (tp) cc_final: 0.7525 (mt) REVERT: A 235 ILE cc_start: 0.7628 (mm) cc_final: 0.7405 (mt) REVERT: B 4 TYR cc_start: 0.8153 (t80) cc_final: 0.7940 (t80) REVERT: B 5 ASP cc_start: 0.8288 (m-30) cc_final: 0.8018 (m-30) REVERT: B 14 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.6862 (mmp-170) REVERT: B 171 ARG cc_start: 0.7391 (ttt-90) cc_final: 0.6602 (ttp-170) REVERT: B 174 LYS cc_start: 0.7774 (mtpm) cc_final: 0.7222 (mtmp) REVERT: B 204 LEU cc_start: 0.7739 (tp) cc_final: 0.7474 (mt) REVERT: C 5 ASP cc_start: 0.8412 (m-30) cc_final: 0.8078 (m-30) REVERT: C 43 MET cc_start: 0.7930 (mtt) cc_final: 0.7695 (mtt) REVERT: C 171 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6382 (ttp-170) REVERT: C 174 LYS cc_start: 0.7698 (mtpm) cc_final: 0.7172 (mtmp) REVERT: C 186 ARG cc_start: 0.7992 (ttt180) cc_final: 0.6898 (ttm110) REVERT: C 204 LEU cc_start: 0.7704 (tp) cc_final: 0.7489 (mt) REVERT: C 230 LEU cc_start: 0.7623 (tp) cc_final: 0.7392 (tp) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 1.5137 time to fit residues: 141.0236 Evaluate side-chains 82 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 165 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/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-dev-5322/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-dev-5322/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-dev-5322/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-dev-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/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-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/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-dev-5322/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-dev-5322/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-dev-5322/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: 70.41 > 50: distance: 63 - 75: 3.010 distance: 65 - 81: 13.013 distance: 70 - 89: 20.900 distance: 74 - 94: 30.730 distance: 77 - 81: 11.603 distance: 78 - 101: 24.139 distance: 81 - 82: 8.146 distance: 82 - 83: 7.450 distance: 82 - 85: 10.921 distance: 83 - 84: 32.805 distance: 83 - 89: 11.366 distance: 84 - 112: 26.914 distance: 85 - 86: 19.634 distance: 85 - 87: 24.188 distance: 89 - 90: 33.843 distance: 90 - 91: 56.119 distance: 90 - 93: 23.500 distance: 91 - 94: 15.166 distance: 92 - 119: 31.896 distance: 94 - 95: 32.888 distance: 95 - 96: 13.057 distance: 95 - 98: 36.503 distance: 96 - 97: 4.878 distance: 96 - 101: 17.746 distance: 97 - 124: 19.068 distance: 98 - 99: 43.261 distance: 98 - 100: 39.134 distance: 101 - 102: 16.301 distance: 102 - 103: 15.089 distance: 102 - 105: 34.845 distance: 103 - 104: 27.896 distance: 103 - 112: 13.141 distance: 104 - 132: 7.720 distance: 105 - 106: 48.646 distance: 106 - 107: 19.692 distance: 106 - 108: 25.225 distance: 107 - 109: 30.548 distance: 108 - 110: 27.242 distance: 109 - 111: 43.185 distance: 110 - 111: 49.489 distance: 112 - 113: 10.281 distance: 113 - 114: 10.426 distance: 113 - 116: 5.429 distance: 114 - 115: 19.541 distance: 114 - 119: 10.238 distance: 115 - 146: 28.154 distance: 116 - 117: 27.364 distance: 116 - 118: 33.585 distance: 120 - 121: 5.027 distance: 120 - 123: 7.825 distance: 121 - 122: 18.209 distance: 121 - 124: 17.298 distance: 122 - 152: 21.928 distance: 124 - 125: 8.396 distance: 125 - 126: 18.568 distance: 125 - 128: 12.559 distance: 126 - 127: 26.037 distance: 126 - 132: 12.360 distance: 127 - 157: 9.812 distance: 128 - 129: 21.398 distance: 129 - 130: 32.003 distance: 129 - 131: 49.417 distance: 132 - 133: 10.082 distance: 133 - 134: 7.708 distance: 133 - 136: 8.132 distance: 134 - 135: 7.187 distance: 134 - 146: 3.672 distance: 135 - 164: 7.221 distance: 136 - 137: 8.160 distance: 137 - 138: 10.987 distance: 137 - 139: 23.661 distance: 138 - 140: 12.696 distance: 139 - 141: 39.744 distance: 139 - 142: 15.766 distance: 140 - 141: 5.725 distance: 141 - 143: 25.580 distance: 142 - 144: 9.665 distance: 143 - 145: 9.993 distance: 144 - 145: 9.549 distance: 147 - 148: 3.088 distance: 147 - 150: 4.153 distance: 148 - 149: 5.976 distance: 148 - 152: 4.509 distance: 150 - 151: 8.208 distance: 153 - 154: 5.490 distance: 153 - 156: 5.036 distance: 154 - 155: 10.312 distance: 154 - 157: 6.515 distance: 155 - 174: 13.089