Starting phenix.real_space_refine on Wed Mar 5 16:36:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.map" model { file = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul5_26592/03_2025/7ul5_26592.cif" } resolution = 3.1 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= 0.088 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 1834 2.51 5 N 449 2.21 5 O 466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2773 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 604 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 85} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.96, per 1000 atoms: 1.07 Number of scatterers: 2773 At special positions: 0 Unit cell: (67.3159, 57.9428, 109.069, 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 466 8.00 N 449 7.00 C 1834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " 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: 0.66 Conformation dependent library (CDL) restraints added in 333.0 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 65.5% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 40 through 71 removed outlier: 3.985A pdb=" N ALA A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 removed outlier: 4.245A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 112 through 146 removed outlier: 3.649A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.940A pdb=" N ALA A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 155 through 180 removed outlier: 3.515A pdb=" N ALA A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.532A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.627A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 282 removed outlier: 3.531A pdb=" N ARG A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 288 through 315 removed outlier: 4.273A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.732A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.687A pdb=" N SER D 23 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 576 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: 0.77 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 842 1.34 - 1.46: 637 1.46 - 1.58: 1320 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 2835 Sorted by residual: bond pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU D 33 " pdb=" CD1 LEU D 33 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.19e-02 7.06e+03 1.10e+00 bond pdb=" CB VAL D 80 " pdb=" CG2 VAL D 80 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " ideal model delta sigma weight residual 1.535 1.555 -0.020 2.02e-02 2.45e+03 9.73e-01 ... (remaining 2830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 3740 1.59 - 3.18: 106 3.18 - 4.77: 20 4.77 - 6.36: 0 6.36 - 7.95: 1 Bond angle restraints: 3867 Sorted by residual: angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 112.68 116.13 -3.45 1.33e+00 5.65e-01 6.71e+00 angle pdb=" N ASN A 308 " pdb=" CA ASN A 308 " pdb=" C ASN A 308 " ideal model delta sigma weight residual 113.16 116.80 -3.64 1.42e+00 4.96e-01 6.57e+00 angle pdb=" CA LEU A 105 " pdb=" CB LEU A 105 " pdb=" CG LEU A 105 " ideal model delta sigma weight residual 116.30 124.25 -7.95 3.50e+00 8.16e-02 5.17e+00 angle pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " pdb=" CG ASP D 111 " ideal model delta sigma weight residual 112.60 114.70 -2.10 1.00e+00 1.00e+00 4.39e+00 angle pdb=" N GLN A 126 " pdb=" CA GLN A 126 " pdb=" C GLN A 126 " ideal model delta sigma weight residual 111.36 113.62 -2.26 1.09e+00 8.42e-01 4.30e+00 ... (remaining 3862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 1455 14.03 - 28.05: 134 28.05 - 42.08: 33 42.08 - 56.10: 4 56.10 - 70.13: 1 Dihedral angle restraints: 1627 sinusoidal: 551 harmonic: 1076 Sorted by residual: dihedral pdb=" CG ARG A 249 " pdb=" CD ARG A 249 " pdb=" NE ARG A 249 " pdb=" CZ ARG A 249 " ideal model delta sinusoidal sigma weight residual 180.00 136.43 43.57 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB MET A 119 " pdb=" CG MET A 119 " pdb=" SD MET A 119 " pdb=" CE MET A 119 " ideal model delta sinusoidal sigma weight residual 60.00 111.66 -51.66 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual -180.00 -164.97 -15.03 0 5.00e+00 4.00e-02 9.03e+00 ... (remaining 1624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 280 0.032 - 0.063: 126 0.063 - 0.095: 41 0.095 - 0.126: 15 0.126 - 0.158: 3 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA PHE A 127 " pdb=" N PHE A 127 " pdb=" C PHE A 127 " pdb=" CB PHE A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 462 not shown) Planarity restraints: 470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 46 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 46 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 46 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 47 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 211 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.10e+00 pdb=" C TYR A 211 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 211 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 212 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 219 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 220 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.028 5.00e-02 4.00e+02 ... (remaining 467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1094 2.90 - 3.40: 2578 3.40 - 3.90: 4120 3.90 - 4.40: 4429 4.40 - 4.90: 8105 Nonbonded interactions: 20326 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" OG1 THR A 47 " model vdw 2.404 3.040 nonbonded pdb=" O GLY A 57 " pdb=" ND2 ASN A 61 " model vdw 2.439 3.120 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 301 " model vdw 2.458 3.040 nonbonded pdb=" OH TYR A 71 " pdb=" OD1 ASN A 325 " model vdw 2.463 3.040 nonbonded pdb=" O ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.521 3.040 ... (remaining 20321 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: 1.610 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.039 2835 Z= 0.251 Angle : 0.639 7.955 3867 Z= 0.363 Chirality : 0.042 0.158 465 Planarity : 0.006 0.050 470 Dihedral : 11.756 70.125 927 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.07 (0.41), residues: 355 helix: 0.01 (0.31), residues: 225 sheet: -0.48 (0.64), residues: 64 loop : -3.07 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 38 HIS 0.003 0.002 HIS A 146 PHE 0.013 0.001 PHE A 217 TYR 0.014 0.002 TYR A 228 ARG 0.003 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.298 Fit side-chains REVERT: A 281 SER cc_start: 0.8448 (t) cc_final: 0.8085 (m) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1158 time to fit residues: 5.0466 Evaluate side-chains 30 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110353 restraints weight = 3240.455| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.84 r_work: 0.3011 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2835 Z= 0.238 Angle : 0.553 6.294 3867 Z= 0.307 Chirality : 0.040 0.125 465 Planarity : 0.005 0.041 470 Dihedral : 3.744 15.326 396 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.37 % Allowed : 6.72 % Favored : 92.91 % 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: 0.97 (0.44), residues: 355 helix: 1.57 (0.33), residues: 224 sheet: -0.08 (0.67), residues: 64 loop : -1.68 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.014 0.001 PHE A 213 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.300 Fit side-chains REVERT: A 281 SER cc_start: 0.8315 (t) cc_final: 0.7897 (m) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.1040 time to fit residues: 4.5520 Evaluate side-chains 33 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1221 > 50: distance: 24 - 36: 19.244 distance: 36 - 37: 28.681 distance: 36 - 42: 24.367 distance: 37 - 38: 26.615 distance: 37 - 40: 19.931 distance: 38 - 39: 3.572 distance: 38 - 43: 19.495 distance: 40 - 41: 12.254 distance: 41 - 42: 30.017 distance: 43 - 44: 34.745 distance: 44 - 45: 5.893 distance: 44 - 47: 15.425 distance: 45 - 46: 28.017 distance: 45 - 54: 14.563 distance: 47 - 48: 18.350 distance: 48 - 49: 12.656 distance: 48 - 50: 22.719 distance: 49 - 51: 17.384 distance: 50 - 52: 9.931 distance: 51 - 53: 16.817 distance: 52 - 53: 18.085 distance: 54 - 55: 32.225 distance: 55 - 56: 19.829 distance: 56 - 57: 11.906 distance: 56 - 58: 11.566 distance: 58 - 59: 7.209 distance: 59 - 60: 6.198 distance: 59 - 62: 6.030 distance: 60 - 61: 5.339 distance: 60 - 67: 8.072 distance: 61 - 86: 8.505 distance: 62 - 63: 4.530 distance: 63 - 64: 7.020 distance: 64 - 65: 14.152 distance: 65 - 66: 14.879 distance: 67 - 68: 3.656 distance: 68 - 69: 9.940 distance: 68 - 71: 9.797 distance: 69 - 70: 15.293 distance: 69 - 72: 7.681 distance: 72 - 73: 3.307 distance: 73 - 74: 5.009 distance: 74 - 75: 4.835 distance: 74 - 80: 12.003 distance: 75 - 104: 23.789 distance: 76 - 77: 14.257 distance: 76 - 78: 13.834 distance: 77 - 79: 7.753 distance: 80 - 81: 10.487 distance: 81 - 82: 15.945 distance: 81 - 84: 3.451 distance: 82 - 83: 10.192 distance: 82 - 86: 5.691 distance: 83 - 111: 6.292 distance: 84 - 85: 16.561 distance: 85 - 161: 5.938 distance: 86 - 87: 3.569 distance: 87 - 88: 13.911 distance: 87 - 90: 10.359 distance: 88 - 89: 14.723 distance: 88 - 97: 7.084 distance: 89 - 119: 20.634 distance: 90 - 91: 14.384 distance: 91 - 92: 5.469 distance: 92 - 93: 5.667 distance: 93 - 94: 7.876 distance: 94 - 95: 3.241 distance: 97 - 98: 6.019 distance: 98 - 99: 4.337 distance: 98 - 101: 7.658 distance: 99 - 104: 9.482 distance: 100 - 126: 15.561 distance: 101 - 102: 12.593 distance: 101 - 103: 19.411 distance: 104 - 105: 13.625 distance: 105 - 106: 3.600 distance: 105 - 108: 5.387 distance: 106 - 107: 5.781 distance: 106 - 111: 7.306 distance: 107 - 133: 13.011 distance: 108 - 109: 6.307 distance: 108 - 110: 18.676