Starting phenix.real_space_refine on Thu Mar 6 00:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1b_33559/03_2025/7y1b_33559_neut.cif" } resolution = 3.23 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= 0.027 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 16 5.16 5 C 2587 2.51 5 N 698 2.21 5 O 836 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: 4137 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 868 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "L" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1661 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 3.32, per 1000 atoms: 0.80 Number of scatterers: 4137 At special positions: 0 Unit cell: (76.44, 65.52, 107.52, 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 16 16.00 O 836 8.00 N 698 7.00 C 2587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 163 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.04 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: 0.94 Conformation dependent library (CDL) restraints added in 486.6 milliseconds 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 3.7% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.294A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 84 removed outlier: 4.213A pdb=" N LYS H 84 " --> pdb=" O GLU H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'L' and resid 99 through 103 removed outlier: 4.095A pdb=" N VAL L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.964A pdb=" N THR A 186 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 28 through 31 removed outlier: 6.558A pdb=" N GLU H 29 " --> pdb=" O THR H 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 78 through 79 removed outlier: 6.687A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 53 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 125 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AA7, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AA8, first strand: chain 'H' and resid 174 through 177 Processing sheet with id=AA9, first strand: chain 'L' and resid 25 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 33 removed outlier: 3.832A pdb=" N TYR L 106 " --> pdb=" O THR L 122 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN L 57 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU L 66 " --> pdb=" O GLN L 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 134 through 138 removed outlier: 3.922A pdb=" N ASN L 157 " --> pdb=" O THR L 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 173 through 174 removed outlier: 6.278A pdb=" N HIS L 218 " --> pdb=" O SER L 223 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER L 223 " --> pdb=" O HIS L 218 " (cutoff:3.500A) 164 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: 1.48 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1331 1.34 - 1.46: 1049 1.46 - 1.58: 1832 1.58 - 1.70: 0 1.70 - 1.82: 21 Bond restraints: 4233 Sorted by residual: bond pdb=" CG PRO H 72 " pdb=" CD PRO H 72 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.29e+00 bond pdb=" CG PRO A 133 " pdb=" CD PRO A 133 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.22e+00 bond pdb=" CZ ARG H 117 " pdb=" NH2 ARG H 117 " ideal model delta sigma weight residual 1.330 1.317 0.013 1.30e-02 5.92e+03 1.07e+00 bond pdb=" CB PRO L 161 " pdb=" CG PRO L 161 " ideal model delta sigma weight residual 1.492 1.443 0.049 5.00e-02 4.00e+02 9.56e-01 bond pdb=" CB GLN H 25 " pdb=" CG GLN H 25 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 ... (remaining 4228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 5475 1.25 - 2.50: 227 2.50 - 3.75: 45 3.75 - 5.00: 13 5.00 - 6.24: 3 Bond angle restraints: 5763 Sorted by residual: angle pdb=" C TYR L 70 " pdb=" N VAL L 71 " pdb=" CA VAL L 71 " ideal model delta sigma weight residual 120.46 116.81 3.65 1.37e+00 5.33e-01 7.11e+00 angle pdb=" N TYR L 160 " pdb=" CA TYR L 160 " pdb=" C TYR L 160 " ideal model delta sigma weight residual 109.81 115.61 -5.80 2.21e+00 2.05e-01 6.88e+00 angle pdb=" N TYR L 70 " pdb=" CA TYR L 70 " pdb=" C TYR L 70 " ideal model delta sigma weight residual 108.23 104.68 3.55 1.38e+00 5.25e-01 6.63e+00 angle pdb=" CA TYR A 132 " pdb=" CB TYR A 132 " pdb=" CG TYR A 132 " ideal model delta sigma weight residual 113.90 109.57 4.33 1.80e+00 3.09e-01 5.80e+00 angle pdb=" N SER L 72 " pdb=" CA SER L 72 " pdb=" C SER L 72 " ideal model delta sigma weight residual 110.80 115.76 -4.96 2.13e+00 2.20e-01 5.43e+00 ... (remaining 5758 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2277 17.56 - 35.12: 214 35.12 - 52.68: 39 52.68 - 70.24: 7 70.24 - 87.79: 3 Dihedral angle restraints: 2540 sinusoidal: 973 harmonic: 1567 Sorted by residual: dihedral pdb=" CA PRO H 170 " pdb=" C PRO H 170 " pdb=" N GLU H 171 " pdb=" CA GLU H 171 " ideal model delta harmonic sigma weight residual -180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR H 79 " pdb=" C TYR H 79 " pdb=" N ASN H 80 " pdb=" CA ASN H 80 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU H 102 " pdb=" C LEU H 102 " pdb=" N SER H 103 " pdb=" CA SER H 103 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 351 0.032 - 0.064: 210 0.064 - 0.095: 46 0.095 - 0.127: 37 0.127 - 0.159: 9 Chirality restraints: 653 Sorted by residual: chirality pdb=" CA ILE L 68 " pdb=" N ILE L 68 " pdb=" C ILE L 68 " pdb=" CB ILE L 68 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ILE A 175 " pdb=" N ILE A 175 " pdb=" C ILE A 175 " pdb=" CB ILE A 175 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 650 not shown) Planarity restraints: 735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 167 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO A 168 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 132 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 133 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 71 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO H 72 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 72 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 72 " -0.020 5.00e-02 4.00e+02 ... (remaining 732 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1514 2.85 - 3.36: 3279 3.36 - 3.88: 6231 3.88 - 4.39: 7142 4.39 - 4.90: 13496 Nonbonded interactions: 31662 Sorted by model distance: nonbonded pdb=" O GLY H 156 " pdb=" OG SER H 157 " model vdw 2.340 3.040 nonbonded pdb=" N ASP A 179 " pdb=" OD2 ASP A 183 " model vdw 2.340 3.120 nonbonded pdb=" NZ LYS H 86 " pdb=" O SER H 104 " model vdw 2.349 3.120 nonbonded pdb=" O SER L 188 " pdb=" OG SER L 188 " model vdw 2.354 3.040 nonbonded pdb=" O SER L 97 " pdb=" OG SER L 97 " model vdw 2.371 3.040 ... (remaining 31657 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: 1.560 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4233 Z= 0.376 Angle : 0.636 6.244 5763 Z= 0.341 Chirality : 0.047 0.159 653 Planarity : 0.005 0.060 735 Dihedral : 14.264 87.794 1519 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.42 (0.35), residues: 533 helix: -3.89 (1.04), residues: 12 sheet: -0.13 (0.31), residues: 258 loop : -1.65 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 66 HIS 0.005 0.001 HIS H 71 PHE 0.009 0.002 PHE L 155 TYR 0.022 0.002 TYR A 132 ARG 0.014 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.480 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1858 time to fit residues: 12.1837 Evaluate side-chains 48 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114854 restraints weight = 5462.029| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.11 r_work: 0.3253 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4233 Z= 0.227 Angle : 0.621 7.921 5763 Z= 0.317 Chirality : 0.046 0.161 653 Planarity : 0.005 0.064 735 Dihedral : 4.679 18.948 578 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.63 % Allowed : 5.49 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.93 (0.36), residues: 533 helix: -3.65 (0.96), residues: 13 sheet: 0.19 (0.31), residues: 261 loop : -1.29 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.001 PHE H 169 TYR 0.014 0.001 TYR A 132 ARG 0.006 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: H 128 GLN cc_start: 0.8728 (tp-100) cc_final: 0.8442 (mm-40) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1801 time to fit residues: 12.3377 Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 0.0170 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.3834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113230 restraints weight = 5494.619| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.10 r_work: 0.3315 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4233 Z= 0.151 Angle : 0.551 6.149 5763 Z= 0.280 Chirality : 0.043 0.159 653 Planarity : 0.005 0.062 735 Dihedral : 4.188 18.009 578 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.42 % Allowed : 8.23 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.36), residues: 533 helix: -3.57 (0.91), residues: 14 sheet: 0.30 (0.31), residues: 258 loop : -1.06 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.009 0.001 PHE A 139 TYR 0.011 0.001 TYR A 132 ARG 0.006 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.462 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 0.1814 time to fit residues: 11.3544 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111357 restraints weight = 5511.077| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.15 r_work: 0.3262 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4233 Z= 0.252 Angle : 0.597 6.804 5763 Z= 0.302 Chirality : 0.045 0.152 653 Planarity : 0.005 0.062 735 Dihedral : 4.417 18.107 578 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.05 % Allowed : 10.34 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.62 (0.37), residues: 533 helix: -3.58 (0.86), residues: 14 sheet: 0.33 (0.31), residues: 259 loop : -0.96 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 138 HIS 0.004 0.001 HIS H 71 PHE 0.008 0.001 PHE L 229 TYR 0.013 0.001 TYR L 70 ARG 0.004 0.001 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7840 (tt0) outliers start: 5 outliers final: 2 residues processed: 52 average time/residue: 0.1593 time to fit residues: 10.6671 Evaluate side-chains 50 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 0.0040 chunk 5 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** L 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119458 restraints weight = 5422.723| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.08 r_work: 0.3310 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4233 Z= 0.151 Angle : 0.536 6.061 5763 Z= 0.272 Chirality : 0.043 0.149 653 Planarity : 0.005 0.062 735 Dihedral : 4.065 17.593 578 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.05 % Allowed : 10.97 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.35 (0.37), residues: 533 helix: -3.47 (0.92), residues: 14 sheet: 0.55 (0.32), residues: 259 loop : -0.83 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.003 0.001 HIS H 71 PHE 0.009 0.001 PHE A 139 TYR 0.009 0.001 TYR L 70 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1066 Ramachandran restraints generated. 533 Oldfield, 0 Emsley, 533 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 114 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7762 (tt0) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.1956 time to fit residues: 12.6009 Evaluate side-chains 47 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 61.9867 > 50: distance: 17 - 128: 34.772 distance: 20 - 125: 26.026 distance: 30 - 114: 13.589 distance: 33 - 111: 25.096 distance: 42 - 102: 10.123 distance: 45 - 99: 3.647 distance: 75 - 108: 34.821 distance: 78 - 105: 19.887 distance: 95 - 99: 6.717 distance: 99 - 100: 7.950 distance: 100 - 101: 12.321 distance: 100 - 103: 21.094 distance: 101 - 102: 14.102 distance: 101 - 105: 12.466 distance: 105 - 106: 16.053 distance: 106 - 107: 24.297 distance: 106 - 109: 5.652 distance: 107 - 108: 22.324 distance: 107 - 111: 36.761 distance: 109 - 110: 8.785 distance: 111 - 112: 36.343 distance: 112 - 113: 32.621 distance: 112 - 115: 23.442 distance: 113 - 114: 15.792 distance: 113 - 118: 4.767 distance: 115 - 116: 17.954 distance: 115 - 117: 6.292 distance: 118 - 119: 17.889 distance: 119 - 120: 17.040 distance: 119 - 122: 30.326 distance: 120 - 121: 11.948 distance: 120 - 125: 9.910 distance: 122 - 123: 13.256 distance: 122 - 124: 30.214 distance: 125 - 126: 13.971 distance: 126 - 127: 8.611 distance: 126 - 129: 30.329 distance: 127 - 128: 33.462 distance: 127 - 132: 6.547 distance: 129 - 130: 38.904 distance: 129 - 131: 33.429 distance: 132 - 133: 16.005 distance: 133 - 134: 33.905 distance: 133 - 136: 37.684 distance: 134 - 135: 23.945 distance: 134 - 139: 29.883 distance: 136 - 137: 36.651 distance: 136 - 138: 30.732 distance: 139 - 140: 13.037 distance: 140 - 141: 26.800 distance: 141 - 142: 41.682 distance: 141 - 145: 10.904 distance: 145 - 146: 6.485 distance: 146 - 147: 28.488 distance: 146 - 149: 8.173 distance: 147 - 148: 14.133 distance: 147 - 151: 27.809 distance: 149 - 150: 26.138 distance: 151 - 152: 33.884 distance: 152 - 153: 24.267 distance: 152 - 155: 20.972 distance: 153 - 154: 13.316 distance: 153 - 158: 10.714 distance: 155 - 156: 11.504 distance: 155 - 157: 3.044 distance: 158 - 159: 10.281 distance: 159 - 160: 13.820 distance: 159 - 162: 18.916 distance: 160 - 161: 7.686 distance: 160 - 172: 20.379 distance: 162 - 163: 35.955 distance: 163 - 164: 31.415 distance: 163 - 165: 24.779 distance: 164 - 166: 6.182 distance: 165 - 167: 10.363 distance: 165 - 168: 4.483 distance: 166 - 167: 7.963 distance: 167 - 169: 13.043 distance: 168 - 170: 9.655 distance: 169 - 171: 3.998 distance: 170 - 171: 4.968