Starting phenix.real_space_refine on Fri May 9 13:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvm_61840/05_2025/9jvm_61840.cif" } resolution = 2.36 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= 0.000 sd= 0.015 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 9 5.16 5 C 1183 2.51 5 N 295 2.21 5 O 313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 1800 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1800 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 18, 'TRANS': 248} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 180 Time building chain proxies: 3.03, per 1000 atoms: 1.68 Number of scatterers: 1800 At special positions: 0 Unit cell: (70.3, 62.16, 55.5, 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 9 16.00 O 313 8.00 N 295 7.00 C 1183 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 - 3.00 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: 0.51 Conformation dependent library (CDL) restraints added in 253.3 milliseconds 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 14 through 47 Proline residue: R 20 - end of helix removed outlier: 3.586A pdb=" N PHE R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR R 29 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU R 30 " --> pdb=" O LEU R 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.520A pdb=" N LEU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 68 removed outlier: 3.824A pdb=" N LEU R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 77 removed outlier: 3.817A pdb=" N TRP R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ASP R 75 " --> pdb=" O PRO R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 120 removed outlier: 4.110A pdb=" N ARG R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 148 removed outlier: 3.551A pdb=" N TRP R 142 " --> pdb=" O SER R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 154 removed outlier: 3.506A pdb=" N LEU R 154 " --> pdb=" O PRO R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 210 Processing helix chain 'R' and resid 225 through 227 No H-bonds generated for 'chain 'R' and resid 225 through 227' Processing helix chain 'R' and resid 228 through 253 removed outlier: 4.017A pdb=" N CYS R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Proline residue: R 240 - end of helix removed outlier: 4.038A pdb=" N PHE R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 294 removed outlier: 4.065A pdb=" N HIS R 276 " --> pdb=" O PHE R 272 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N CYS R 286 " --> pdb=" O ALA R 282 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 296 through 308 removed outlier: 4.453A pdb=" N ALA R 300 " --> pdb=" O ALA R 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG R 301 " --> pdb=" O CYS R 297 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 408 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: 0.53 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 474 1.33 - 1.45: 344 1.45 - 1.57: 1013 1.57 - 1.69: 0 1.69 - 1.81: 11 Bond restraints: 1842 Sorted by residual: bond pdb=" CB PHE R 272 " pdb=" CG PHE R 272 " ideal model delta sigma weight residual 1.502 1.464 0.038 2.30e-02 1.89e+03 2.78e+00 bond pdb=" C PHE R 272 " pdb=" N PRO R 273 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 bond pdb=" CB VAL R 96 " pdb=" CG1 VAL R 96 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.34e+00 bond pdb=" C LEU R 281 " pdb=" O LEU R 281 " ideal model delta sigma weight residual 1.236 1.253 -0.016 1.15e-02 7.56e+03 2.02e+00 bond pdb=" CB TYR R 55 " pdb=" CG TYR R 55 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.20e-02 2.07e+03 1.91e+00 ... (remaining 1837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 2428 2.43 - 4.86: 91 4.86 - 7.29: 19 7.29 - 9.72: 3 9.72 - 12.15: 1 Bond angle restraints: 2542 Sorted by residual: angle pdb=" CA PRO R 20 " pdb=" N PRO R 20 " pdb=" CD PRO R 20 " ideal model delta sigma weight residual 112.00 106.03 5.97 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA LEU R 244 " pdb=" CB LEU R 244 " pdb=" CG LEU R 244 " ideal model delta sigma weight residual 116.30 128.45 -12.15 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CA ARG R 207 " pdb=" CB ARG R 207 " pdb=" CG ARG R 207 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA PRO R 21 " pdb=" N PRO R 21 " pdb=" CD PRO R 21 " ideal model delta sigma weight residual 112.00 107.22 4.78 1.40e+00 5.10e-01 1.17e+01 angle pdb=" CA PRO R 33 " pdb=" N PRO R 33 " pdb=" CD PRO R 33 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 ... (remaining 2537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 951 14.84 - 29.67: 89 29.67 - 44.51: 19 44.51 - 59.34: 1 59.34 - 74.18: 2 Dihedral angle restraints: 1062 sinusoidal: 295 harmonic: 767 Sorted by residual: dihedral pdb=" CA PRO R 71 " pdb=" C PRO R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA TYR R 172 " pdb=" C TYR R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU R 123 " pdb=" C LEU R 123 " pdb=" N ARG R 124 " pdb=" CA ARG R 124 " ideal model delta harmonic sigma weight residual -180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 1059 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.037: 173 0.037 - 0.074: 93 0.074 - 0.111: 35 0.111 - 0.147: 14 0.147 - 0.184: 2 Chirality restraints: 317 Sorted by residual: chirality pdb=" CG LEU R 66 " pdb=" CB LEU R 66 " pdb=" CD1 LEU R 66 " pdb=" CD2 LEU R 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CB ILE R 158 " pdb=" CA ILE R 158 " pdb=" CG1 ILE R 158 " pdb=" CG2 ILE R 158 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA PRO R 72 " pdb=" N PRO R 72 " pdb=" C PRO R 72 " pdb=" CB PRO R 72 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 314 not shown) Planarity restraints: 321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 32 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO R 33 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO R 33 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 33 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 19 " -0.069 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 20 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 20 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO R 20 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 71 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO R 72 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " 0.043 5.00e-02 4.00e+02 ... (remaining 318 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 301 2.75 - 3.29: 1823 3.29 - 3.82: 2970 3.82 - 4.36: 3061 4.36 - 4.90: 5332 Nonbonded interactions: 13487 Sorted by model distance: nonbonded pdb=" O ARG R 160 " pdb=" N TYR R 172 " model vdw 2.211 3.120 nonbonded pdb=" O ASP R 75 " pdb=" N ARG R 79 " model vdw 2.285 3.120 nonbonded pdb=" O HIS R 165 " pdb=" NE2 HIS R 276 " model vdw 2.361 3.120 nonbonded pdb=" OH TYR R 238 " pdb=" OD1 ASN R 285 " model vdw 2.493 3.040 nonbonded pdb=" O TRP R 43 " pdb=" N VAL R 46 " model vdw 2.496 3.120 ... (remaining 13482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.390 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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 : 0.009 0.064 1842 Z= 0.383 Angle : 1.113 12.147 2542 Z= 0.570 Chirality : 0.054 0.184 317 Planarity : 0.012 0.111 321 Dihedral : 12.646 74.178 570 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.20 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.75 (0.51), residues: 259 helix: 0.05 (0.36), residues: 187 sheet: None (None), residues: 0 loop : -4.48 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 142 HIS 0.007 0.003 HIS R 242 PHE 0.023 0.003 PHE R 272 TYR 0.017 0.002 TYR R 85 ARG 0.015 0.002 ARG R 207 Details of bonding type rmsd hydrogen bonds : bond 0.13856 ( 139) hydrogen bonds : angle 5.90175 ( 408) covalent geometry : bond 0.00881 ( 1842) covalent geometry : angle 1.11331 ( 2542) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.198 Fit side-chains REVERT: R 77 TYR cc_start: 0.5003 (t80) cc_final: 0.4730 (t80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.5406 time to fit residues: 14.1828 Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.0980 chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 23 optimal weight: 0.0270 chunk 16 optimal weight: 0.3980 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.193050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.182868 restraints weight = 3155.219| |-----------------------------------------------------------------------------| r_work (start): 0.4540 rms_B_bonded: 1.87 r_work: 0.4481 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4383 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 1842 Z= 0.163 Angle : 0.806 7.547 2542 Z= 0.386 Chirality : 0.040 0.123 317 Planarity : 0.010 0.072 321 Dihedral : 5.024 20.234 279 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.00 % Allowed : 12.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.53), residues: 259 helix: 1.32 (0.38), residues: 188 sheet: None (None), residues: 0 loop : -3.89 (0.60), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 43 HIS 0.003 0.001 HIS R 276 PHE 0.004 0.001 PHE R 95 TYR 0.021 0.001 TYR R 169 ARG 0.001 0.000 ARG R 132 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 139) hydrogen bonds : angle 4.27878 ( 408) covalent geometry : bond 0.00357 ( 1842) covalent geometry : angle 0.80563 ( 2542) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.184 Fit side-chains REVERT: R 244 LEU cc_start: 0.3948 (tp) cc_final: 0.3357 (tp) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.5521 time to fit residues: 14.4795 Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.188918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.178324 restraints weight = 3085.859| |-----------------------------------------------------------------------------| r_work (start): 0.4498 rms_B_bonded: 1.94 r_work: 0.4434 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4330 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 1842 Z= 0.212 Angle : 0.807 6.395 2542 Z= 0.403 Chirality : 0.043 0.130 317 Planarity : 0.010 0.066 321 Dihedral : 5.147 21.945 279 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.67 % Allowed : 14.67 % Favored : 82.67 % 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: 0.05 (0.54), residues: 259 helix: 1.34 (0.38), residues: 189 sheet: None (None), residues: 0 loop : -3.83 (0.62), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 43 HIS 0.004 0.001 HIS R 242 PHE 0.012 0.001 PHE R 272 TYR 0.011 0.001 TYR R 98 ARG 0.002 0.000 ARG R 248 Details of bonding type rmsd hydrogen bonds : bond 0.05831 ( 139) hydrogen bonds : angle 4.41273 ( 408) covalent geometry : bond 0.00488 ( 1842) covalent geometry : angle 0.80689 ( 2542) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.167 Fit side-chains REVERT: R 244 LEU cc_start: 0.4099 (tp) cc_final: 0.3154 (mt) outliers start: 4 outliers final: 2 residues processed: 25 average time/residue: 0.4744 time to fit residues: 12.5055 Evaluate side-chains 25 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.191545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.181073 restraints weight = 3069.951| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.91 r_work: 0.4462 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4361 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1842 Z= 0.172 Angle : 0.765 6.814 2542 Z= 0.371 Chirality : 0.041 0.129 317 Planarity : 0.009 0.060 321 Dihedral : 4.805 20.426 279 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.33 % Allowed : 16.00 % Favored : 80.67 % 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: 0.27 (0.54), residues: 259 helix: 1.51 (0.39), residues: 190 sheet: None (None), residues: 0 loop : -3.85 (0.60), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 PHE 0.005 0.001 PHE R 95 TYR 0.008 0.001 TYR R 98 ARG 0.001 0.000 ARG R 248 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 139) hydrogen bonds : angle 4.16715 ( 408) covalent geometry : bond 0.00404 ( 1842) covalent geometry : angle 0.76452 ( 2542) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.188 Fit side-chains REVERT: R 66 LEU cc_start: 0.7128 (mm) cc_final: 0.6874 (mm) REVERT: R 244 LEU cc_start: 0.3864 (tp) cc_final: 0.2954 (mt) outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 0.5752 time to fit residues: 16.2273 Evaluate side-chains 24 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 11 optimal weight: 0.0000 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.191015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.180437 restraints weight = 3210.505| |-----------------------------------------------------------------------------| r_work (start): 0.4519 rms_B_bonded: 1.99 r_work: 0.4455 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1842 Z= 0.173 Angle : 0.777 10.057 2542 Z= 0.370 Chirality : 0.042 0.138 317 Planarity : 0.009 0.057 321 Dihedral : 4.722 20.264 279 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.67 % Allowed : 21.33 % Favored : 76.00 % 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: 0.71 (0.55), residues: 259 helix: 1.67 (0.39), residues: 187 sheet: None (None), residues: 0 loop : -2.91 (0.70), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 PHE 0.006 0.001 PHE R 95 TYR 0.009 0.001 TYR R 98 ARG 0.002 0.000 ARG R 207 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 139) hydrogen bonds : angle 4.12582 ( 408) covalent geometry : bond 0.00406 ( 1842) covalent geometry : angle 0.77714 ( 2542) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 518 Ramachandran restraints generated. 259 Oldfield, 0 Emsley, 259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.189 Fit side-chains REVERT: R 244 LEU cc_start: 0.3669 (tp) cc_final: 0.3118 (mt) outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 0.5096 time to fit residues: 12.9653 Evaluate side-chains 23 residues out of total 207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 286 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 50.3309 > 50: distance: 25 - 30: 17.416 distance: 30 - 31: 15.610 distance: 31 - 32: 15.664 distance: 31 - 34: 30.616 distance: 32 - 33: 19.215 distance: 32 - 35: 25.044 distance: 35 - 36: 21.438 distance: 36 - 37: 15.432 distance: 36 - 39: 12.640 distance: 37 - 38: 31.509 distance: 37 - 40: 38.158 distance: 40 - 41: 32.579 distance: 41 - 42: 12.459 distance: 41 - 44: 22.225 distance: 42 - 43: 30.177 distance: 43 - 56: 26.197 distance: 45 - 46: 4.018 distance: 45 - 51: 17.561 distance: 46 - 47: 10.313 distance: 46 - 49: 8.891 distance: 47 - 48: 7.615 distance: 47 - 52: 3.836 distance: 48 - 61: 14.321 distance: 49 - 50: 16.446 distance: 50 - 51: 7.918 distance: 52 - 53: 8.431 distance: 53 - 54: 12.080 distance: 54 - 55: 19.812 distance: 54 - 56: 19.527 distance: 56 - 57: 12.564 distance: 57 - 58: 6.941 distance: 57 - 60: 27.438 distance: 58 - 59: 13.457 distance: 58 - 61: 8.702 distance: 61 - 62: 4.096 distance: 62 - 63: 5.883 distance: 62 - 65: 3.734 distance: 63 - 64: 7.357 distance: 63 - 72: 5.471 distance: 65 - 66: 9.551 distance: 66 - 67: 9.325 distance: 69 - 70: 3.718 distance: 69 - 71: 3.404 distance: 72 - 73: 3.159 distance: 72 - 78: 3.353 distance: 73 - 74: 4.870 distance: 74 - 75: 6.076 distance: 74 - 79: 4.448 distance: 75 - 104: 11.422 distance: 76 - 77: 7.042 distance: 77 - 78: 3.834 distance: 79 - 80: 7.220 distance: 80 - 81: 6.186 distance: 81 - 82: 3.886 distance: 81 - 87: 6.764 distance: 82 - 109: 5.267 distance: 83 - 84: 8.932 distance: 90 - 114: 5.582 distance: 92 - 93: 3.630