Starting phenix.real_space_refine on Thu Jul 18 16:56:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vu8_32126/07_2024/7vu8_32126.cif" } resolution = 3.0 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= 0.006 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 1 5.49 5 S 5 5.16 5 C 914 2.51 5 N 251 2.21 5 O 262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 62": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 1433 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1411 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'ACK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.96, per 1000 atoms: 1.37 Number of scatterers: 1433 At special positions: 0 Unit cell: (66.066, 54.054, 48.048, 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 5 16.00 P 1 15.00 O 262 8.00 N 251 7.00 C 914 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=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 244.7 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 50.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.681A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 129 through 146 removed outlier: 4.028A pdb=" N LEU B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 138 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.683A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.061A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.817A pdb=" N HIS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.452A pdb=" N PHE B 64 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 118 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 41 hydrogen bonds defined for protein. 123 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: 0.31 Time building geometry restraints manager: 0.56 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: 341 1.33 - 1.45: 326 1.45 - 1.57: 796 1.57 - 1.69: 2 1.69 - 1.81: 7 Bond restraints: 1472 Sorted by residual: bond pdb=" O3P ACK B 301 " pdb=" P ACK B 301 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C PHE B 76 " pdb=" O PHE B 76 " ideal model delta sigma weight residual 1.235 1.288 -0.054 1.23e-02 6.61e+03 1.89e+01 bond pdb=" C THR B 77 " pdb=" O THR B 77 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.06e+01 ... (remaining 1467 not shown) Histogram of bond angle deviations from ideal: 92.92 - 101.14: 3 101.14 - 109.35: 125 109.35 - 117.56: 939 117.56 - 125.77: 887 125.77 - 133.98: 33 Bond angle restraints: 1987 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" N TYR B 87 " pdb=" CA TYR B 87 " pdb=" C TYR B 87 " ideal model delta sigma weight residual 113.02 107.90 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU B 98 " pdb=" CA LEU B 98 " pdb=" CB LEU B 98 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" CA VAL B 63 " pdb=" C VAL B 63 " pdb=" O VAL B 63 " ideal model delta sigma weight residual 121.49 117.79 3.70 1.01e+00 9.80e-01 1.34e+01 angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 114.39 109.10 5.29 1.45e+00 4.76e-01 1.33e+01 ... (remaining 1982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 868 31.13 - 62.26: 25 62.26 - 93.39: 0 93.39 - 124.51: 2 124.51 - 155.64: 2 Dihedral angle restraints: 897 sinusoidal: 400 harmonic: 497 Sorted by residual: dihedral pdb=" C2' ACK B 301 " pdb=" O2' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 124.10 -80.26 -155.64 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 234.46 79.07 155.39 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O3P ACK B 301 " ideal model delta sinusoidal sigma weight residual 105.56 -157.87 -96.57 1 3.00e+01 1.11e-03 1.19e+01 ... (remaining 894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 124 0.047 - 0.094: 51 0.094 - 0.141: 18 0.141 - 0.188: 5 0.188 - 0.236: 6 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS B 100 " pdb=" N LYS B 100 " pdb=" C LYS B 100 " pdb=" CB LYS B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 201 not shown) Planarity restraints: 251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO B 70 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 71 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 86 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TYR B 86 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 86 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 87 " -0.011 2.00e-02 2.50e+03 ... (remaining 248 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 407 2.83 - 3.34: 1290 3.34 - 3.86: 2123 3.86 - 4.38: 2502 4.38 - 4.90: 3971 Nonbonded interactions: 10293 Sorted by model distance: nonbonded pdb=" OD1 ASP B 182 " pdb=" N GLY B 183 " model vdw 2.308 2.520 nonbonded pdb=" OE2 GLU B 138 " pdb=" NH2 ARG B 141 " model vdw 2.308 2.520 nonbonded pdb=" CD2 LEU B 98 " pdb=" N ARG B 99 " model vdw 2.426 3.540 nonbonded pdb=" NE ARG B 164 " pdb=" O GLY B 197 " model vdw 2.428 2.520 nonbonded pdb=" O ALA B 219 " pdb=" OG SER B 223 " model vdw 2.436 2.440 ... (remaining 10288 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: 0.840 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.400 Find NCS groups from input model: 0.030 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:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 0.108 1472 Z= 0.636 Angle : 1.189 10.589 1987 Z= 0.809 Chirality : 0.069 0.236 204 Planarity : 0.005 0.033 251 Dihedral : 16.690 155.641 577 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.64 % Allowed : 7.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.46), residues: 168 helix: -3.13 (0.41), residues: 66 sheet: -5.55 (0.71), residues: 19 loop : -3.25 (0.52), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 165 PHE 0.007 0.001 PHE B 83 TYR 0.007 0.001 TYR B 87 ARG 0.003 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.192 Fit side-chains REVERT: B 72 THR cc_start: 0.8243 (p) cc_final: 0.8016 (p) REVERT: B 86 TYR cc_start: 0.7721 (m-80) cc_final: 0.7138 (t80) REVERT: B 119 VAL cc_start: 0.8934 (t) cc_final: 0.8672 (m) outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 0.7811 time to fit residues: 39.1784 Evaluate side-chains 24 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1472 Z= 0.170 Angle : 0.562 5.151 1987 Z= 0.287 Chirality : 0.045 0.132 204 Planarity : 0.003 0.023 251 Dihedral : 17.927 138.608 220 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 7.28 % Allowed : 18.54 % Favored : 74.17 % 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: -3.20 (0.58), residues: 168 helix: -0.80 (0.57), residues: 70 sheet: -4.72 (0.89), residues: 19 loop : -2.66 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 189 HIS 0.003 0.001 HIS B 165 PHE 0.013 0.001 PHE B 92 TYR 0.010 0.001 TYR B 156 ARG 0.001 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 29 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: B 86 TYR cc_start: 0.7759 (m-80) cc_final: 0.7170 (t80) outliers start: 11 outliers final: 4 residues processed: 34 average time/residue: 0.7551 time to fit residues: 26.3713 Evaluate side-chains 27 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1472 Z= 0.120 Angle : 0.513 8.277 1987 Z= 0.250 Chirality : 0.044 0.128 204 Planarity : 0.004 0.056 251 Dihedral : 17.891 150.602 220 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.96 % Allowed : 19.87 % Favored : 74.17 % 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: -2.20 (0.65), residues: 168 helix: 0.26 (0.63), residues: 72 sheet: -4.20 (1.00), residues: 19 loop : -2.42 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 189 HIS 0.002 0.001 HIS B 177 PHE 0.006 0.001 PHE B 92 TYR 0.004 0.001 TYR B 156 ARG 0.001 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 23 time to evaluate : 0.169 Fit side-chains REVERT: B 78 ASP cc_start: 0.8173 (m-30) cc_final: 0.7768 (t0) REVERT: B 86 TYR cc_start: 0.7760 (m-80) cc_final: 0.7132 (t80) REVERT: B 150 ILE cc_start: 0.8905 (pt) cc_final: 0.8531 (pp) outliers start: 9 outliers final: 2 residues processed: 31 average time/residue: 0.8526 time to fit residues: 27.1684 Evaluate side-chains 21 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1472 Z= 0.157 Angle : 0.540 7.547 1987 Z= 0.262 Chirality : 0.045 0.128 204 Planarity : 0.004 0.049 251 Dihedral : 18.018 153.790 220 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.64 % Allowed : 22.52 % Favored : 72.85 % 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: -1.95 (0.64), residues: 168 helix: 0.63 (0.63), residues: 73 sheet: -4.16 (0.99), residues: 19 loop : -2.49 (0.61), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 202 HIS 0.003 0.001 HIS B 177 PHE 0.008 0.001 PHE B 76 TYR 0.006 0.001 TYR B 118 ARG 0.006 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 23 time to evaluate : 0.168 Fit side-chains REVERT: B 78 ASP cc_start: 0.8403 (m-30) cc_final: 0.7874 (t0) REVERT: B 86 TYR cc_start: 0.7661 (m-80) cc_final: 0.7019 (t80) REVERT: B 130 LYS cc_start: 0.2754 (pttt) cc_final: 0.1960 (mttp) REVERT: B 150 ILE cc_start: 0.8914 (pt) cc_final: 0.8513 (pp) outliers start: 7 outliers final: 6 residues processed: 28 average time/residue: 0.8853 time to fit residues: 25.3942 Evaluate side-chains 26 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 1472 Z= 0.214 Angle : 0.558 6.263 1987 Z= 0.282 Chirality : 0.046 0.135 204 Planarity : 0.004 0.044 251 Dihedral : 18.135 154.417 220 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.61 % Allowed : 16.56 % Favored : 74.83 % 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: -2.03 (0.63), residues: 168 helix: 0.69 (0.64), residues: 73 sheet: -4.38 (0.91), residues: 19 loop : -2.63 (0.59), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 131 HIS 0.003 0.001 HIS B 165 PHE 0.007 0.001 PHE B 67 TYR 0.009 0.001 TYR B 118 ARG 0.005 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 24 time to evaluate : 0.169 Fit side-chains REVERT: B 78 ASP cc_start: 0.8570 (m-30) cc_final: 0.7961 (t0) REVERT: B 86 TYR cc_start: 0.7609 (m-80) cc_final: 0.6970 (t80) REVERT: B 130 LYS cc_start: 0.2556 (pttt) cc_final: 0.1836 (mttp) REVERT: B 226 SER cc_start: 0.4756 (t) cc_final: 0.4187 (m) outliers start: 13 outliers final: 9 residues processed: 34 average time/residue: 0.7152 time to fit residues: 24.9905 Evaluate side-chains 30 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 21 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1472 Z= 0.123 Angle : 0.523 6.603 1987 Z= 0.244 Chirality : 0.043 0.128 204 Planarity : 0.004 0.041 251 Dihedral : 18.319 161.714 220 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.97 % Allowed : 22.52 % Favored : 73.51 % 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: -2.07 (0.62), residues: 168 helix: 0.44 (0.61), residues: 80 sheet: -3.96 (0.97), residues: 19 loop : -2.82 (0.57), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 131 HIS 0.002 0.001 HIS B 165 PHE 0.004 0.001 PHE B 67 TYR 0.008 0.001 TYR B 126 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.165 Fit side-chains REVERT: B 78 ASP cc_start: 0.8510 (m-30) cc_final: 0.7871 (t0) REVERT: B 86 TYR cc_start: 0.7544 (m-80) cc_final: 0.6877 (t80) REVERT: B 130 LYS cc_start: 0.2604 (pttt) cc_final: 0.1920 (mttp) REVERT: B 150 ILE cc_start: 0.8945 (pt) cc_final: 0.8553 (pp) REVERT: B 226 SER cc_start: 0.4722 (t) cc_final: 0.4166 (m) outliers start: 6 outliers final: 5 residues processed: 22 average time/residue: 0.7274 time to fit residues: 16.5203 Evaluate side-chains 21 residues out of total 151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.4335 > 50: distance: 80 - 84: 15.138 distance: 84 - 85: 20.267 distance: 85 - 86: 8.933 distance: 85 - 88: 9.214 distance: 86 - 87: 4.827 distance: 86 - 93: 14.519 distance: 88 - 89: 24.503 distance: 89 - 90: 19.977 distance: 90 - 91: 23.167 distance: 91 - 92: 21.536 distance: 93 - 94: 35.285 distance: 94 - 95: 18.675 distance: 94 - 97: 6.336 distance: 95 - 96: 33.903 distance: 95 - 101: 7.223 distance: 97 - 98: 18.341 distance: 97 - 99: 10.069 distance: 98 - 100: 24.295 distance: 101 - 102: 9.650 distance: 102 - 103: 4.967 distance: 102 - 105: 33.139 distance: 103 - 104: 9.673 distance: 103 - 111: 7.814 distance: 105 - 106: 14.170 distance: 106 - 107: 8.565 distance: 106 - 108: 24.151 distance: 107 - 109: 25.283 distance: 108 - 110: 24.014 distance: 109 - 110: 17.128 distance: 111 - 112: 37.917 distance: 112 - 113: 8.164 distance: 112 - 115: 16.666 distance: 113 - 114: 13.226 distance: 113 - 118: 10.611 distance: 115 - 116: 40.017 distance: 115 - 117: 56.113 distance: 118 - 119: 39.111 distance: 119 - 120: 21.917 distance: 119 - 122: 30.012 distance: 120 - 121: 20.301 distance: 120 - 129: 22.211 distance: 122 - 123: 10.160 distance: 123 - 124: 29.137 distance: 123 - 125: 18.072 distance: 124 - 126: 28.279 distance: 125 - 127: 38.708 distance: 126 - 128: 25.757 distance: 127 - 128: 11.985 distance: 129 - 130: 42.538 distance: 130 - 131: 21.426 distance: 130 - 133: 34.050 distance: 131 - 132: 8.887 distance: 131 - 140: 26.045 distance: 133 - 134: 22.789 distance: 134 - 135: 25.933 distance: 135 - 136: 5.374 distance: 136 - 137: 3.242 distance: 137 - 138: 4.019 distance: 137 - 139: 3.062 distance: 140 - 141: 31.418 distance: 141 - 142: 6.716 distance: 141 - 144: 32.566 distance: 142 - 148: 39.249 distance: 144 - 145: 34.991 distance: 145 - 146: 33.280 distance: 145 - 147: 51.332 distance: 148 - 149: 4.972 distance: 149 - 152: 4.113 distance: 150 - 156: 18.645 distance: 152 - 153: 21.733 distance: 153 - 154: 10.223 distance: 153 - 155: 6.988 distance: 156 - 157: 26.901 distance: 157 - 158: 5.968 distance: 157 - 160: 21.159 distance: 158 - 159: 43.051 distance: 158 - 164: 22.421 distance: 160 - 161: 17.977 distance: 161 - 162: 14.826 distance: 161 - 163: 15.882 distance: 164 - 165: 42.822 distance: 165 - 166: 12.604 distance: 165 - 168: 55.381 distance: 166 - 167: 40.220 distance: 166 - 173: 29.636 distance: 168 - 169: 3.714 distance: 169 - 170: 13.680 distance: 170 - 171: 32.333 distance: 170 - 172: 37.944