Starting phenix.real_space_refine on Tue Jan 14 00:30:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.map" model { file = "/net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eke_28200/01_2025/8eke_28200.cif" } resolution = 3.36 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= 0.014 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 42 5.16 5 C 2966 2.51 5 N 791 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2343 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 291} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 3.50, per 1000 atoms: 0.75 Number of scatterers: 4681 At special positions: 0 Unit cell: (89.046, 68.967, 79.443, 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 42 16.00 O 882 8.00 N 791 7.00 C 2966 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: 1.08 Conformation dependent library (CDL) restraints added in 578.9 milliseconds 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1116 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 29.8% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.619A pdb=" N LEU A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.901A pdb=" N LEU A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.621A pdb=" N VAL A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.886A pdb=" N PHE A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 13 through 15 No H-bonds generated for 'chain 'B' and resid 13 through 15' Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.567A pdb=" N LEU B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.792A pdb=" N LEU B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 removed outlier: 4.127A pdb=" N VAL B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.921A pdb=" N PHE B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 8.783A pdb=" N ASN A 28 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.492A pdb=" N GLY A 149 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 148 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 115 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE A 152 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR A 111 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 112 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN A 127 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 114 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 125 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 116 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 7.041A pdb=" N ALA A 173 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 8.786A pdb=" N ASN B 28 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 removed outlier: 6.471A pdb=" N GLY B 149 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 148 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 115 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 152 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.426A pdb=" N THR B 111 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 112 " --> pdb=" O GLN B 127 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN B 127 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 114 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 125 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 116 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103 183 hydrogen bonds defined for protein. 504 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: 1.29 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1544 1.34 - 1.46: 1084 1.46 - 1.58: 2095 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 4785 Sorted by residual: bond pdb=" C ILE A 78 " pdb=" O ILE A 78 " ideal model delta sigma weight residual 1.241 1.232 0.009 1.06e-02 8.90e+03 7.02e-01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.16e-01 bond pdb=" CB PRO A 99 " pdb=" CG PRO A 99 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.86e-01 bond pdb=" CB PRO A 52 " pdb=" CG PRO A 52 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.81e-01 bond pdb=" CA PRO A 184 " pdb=" C PRO A 184 " ideal model delta sigma weight residual 1.527 1.520 0.007 1.07e-02 8.73e+03 3.81e-01 ... (remaining 4780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 6175 0.84 - 1.69: 268 1.69 - 2.53: 29 2.53 - 3.38: 27 3.38 - 4.22: 10 Bond angle restraints: 6509 Sorted by residual: angle pdb=" N ILE B 43 " pdb=" CA ILE B 43 " pdb=" C ILE B 43 " ideal model delta sigma weight residual 113.07 108.97 4.10 1.36e+00 5.41e-01 9.10e+00 angle pdb=" C GLU A 166 " pdb=" N LEU A 167 " pdb=" CA LEU A 167 " ideal model delta sigma weight residual 121.03 118.16 2.87 1.60e+00 3.91e-01 3.22e+00 angle pdb=" CA PRO A 184 " pdb=" C PRO A 184 " pdb=" O PRO A 184 " ideal model delta sigma weight residual 123.16 120.49 2.67 1.49e+00 4.50e-01 3.21e+00 angle pdb=" N VAL A 247 " pdb=" CA VAL A 247 " pdb=" C VAL A 247 " ideal model delta sigma weight residual 113.16 110.58 2.58 1.49e+00 4.50e-01 2.99e+00 angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 113.16 110.71 2.45 1.49e+00 4.50e-01 2.71e+00 ... (remaining 6504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.75: 2615 13.75 - 27.50: 135 27.50 - 41.26: 40 41.26 - 55.01: 16 55.01 - 68.76: 5 Dihedral angle restraints: 2811 sinusoidal: 1065 harmonic: 1746 Sorted by residual: dihedral pdb=" CA ASN B 53 " pdb=" C ASN B 53 " pdb=" N TYR B 54 " pdb=" CA TYR B 54 " ideal model delta harmonic sigma weight residual 180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA MET A 264 " pdb=" CB MET A 264 " pdb=" CG MET A 264 " pdb=" SD MET A 264 " ideal model delta sinusoidal sigma weight residual 60.00 119.11 -59.11 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 60 " pdb=" CB ARG A 60 " pdb=" CG ARG A 60 " pdb=" CD ARG A 60 " ideal model delta sinusoidal sigma weight residual 180.00 127.49 52.51 3 1.50e+01 4.44e-03 9.12e+00 ... (remaining 2808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 405 0.023 - 0.046: 184 0.046 - 0.070: 88 0.070 - 0.093: 34 0.093 - 0.116: 29 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA VAL B 35 " pdb=" N VAL B 35 " pdb=" C VAL B 35 " pdb=" CB VAL B 35 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 ... (remaining 737 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 251 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO B 252 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 251 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 252 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 38 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO B 39 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.015 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1520 2.83 - 3.35: 4130 3.35 - 3.87: 7287 3.87 - 4.38: 8302 4.38 - 4.90: 14609 Nonbonded interactions: 35848 Sorted by model distance: nonbonded pdb=" OG SER A 254 " pdb=" O ILE A 259 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 209 " pdb=" O ILE B 259 " model vdw 2.341 3.040 nonbonded pdb=" N ASN B 28 " pdb=" OD1 ASN B 28 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN A 133 " pdb=" OG1 THR A 135 " model vdw 2.381 3.040 nonbonded pdb=" N ASP B 263 " pdb=" OD1 ASP B 263 " model vdw 2.384 3.120 ... (remaining 35843 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 206 or (resid 207 and (name N or name CA or name \ C or name O or name CB )) or resid 208 through 305)) selection = (chain 'B' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 305)) } 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: 1.900 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.310 Find NCS groups from input model: 0.180 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.002 0.039 4785 Z= 0.117 Angle : 0.447 4.222 6509 Z= 0.245 Chirality : 0.038 0.116 740 Planarity : 0.003 0.036 848 Dihedral : 10.502 68.761 1695 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % Rotamer: Outliers : 2.71 % Allowed : 8.53 % Favored : 88.76 % 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: -0.29 (0.34), residues: 606 helix: 0.58 (0.44), residues: 162 sheet: -0.49 (0.48), residues: 106 loop : -0.40 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 207 HIS 0.002 0.000 HIS B 64 PHE 0.005 0.001 PHE A 230 TYR 0.006 0.001 TYR A 239 ARG 0.001 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7014 (ptpt) cc_final: 0.6792 (ptpt) REVERT: A 222 ARG cc_start: 0.5648 (mmm-85) cc_final: 0.5407 (mmm-85) REVERT: B 49 MET cc_start: 0.4720 (tpp) cc_final: 0.4484 (tpp) REVERT: B 93 THR cc_start: 0.8797 (m) cc_final: 0.8574 (p) REVERT: B 222 ARG cc_start: 0.5722 (mmm-85) cc_final: 0.5442 (mmm-85) REVERT: B 238 ASN cc_start: 0.7391 (t0) cc_final: 0.7183 (t0) outliers start: 14 outliers final: 5 residues processed: 156 average time/residue: 0.1928 time to fit residues: 36.9224 Evaluate side-chains 105 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 263 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.0000 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN B 28 ASN B 84 ASN B 110 GLN B 180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.161310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.148370 restraints weight = 9777.678| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 3.53 r_work: 0.3949 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4785 Z= 0.276 Angle : 0.623 7.154 6509 Z= 0.327 Chirality : 0.044 0.176 740 Planarity : 0.004 0.034 848 Dihedral : 5.034 45.071 659 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % Rotamer: Outliers : 6.40 % Allowed : 15.70 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.34), residues: 606 helix: 0.44 (0.43), residues: 164 sheet: -1.10 (0.50), residues: 82 loop : -0.63 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 207 HIS 0.003 0.001 HIS B 172 PHE 0.026 0.001 PHE A 230 TYR 0.020 0.002 TYR A 239 ARG 0.002 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1212 Ramachandran restraints generated. 606 Oldfield, 0 Emsley, 606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8960 (tpp) cc_final: 0.8683 (ttm) REVERT: A 77 VAL cc_start: 0.5316 (OUTLIER) cc_final: 0.4964 (m) REVERT: A 102 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8343 (mmmt) REVERT: A 207 TRP cc_start: 0.9012 (t60) cc_final: 0.8262 (t60) REVERT: A 222 ARG cc_start: 0.6197 (mmm-85) cc_final: 0.5899 (mmm-85) REVERT: A 247 VAL cc_start: 0.4561 (OUTLIER) cc_final: 0.4344 (p) REVERT: B 28 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7883 (p0) REVERT: B 49 MET cc_start: 0.5217 (tpp) cc_final: 0.4987 (tpt) REVERT: B 91 VAL cc_start: 0.4646 (OUTLIER) cc_final: 0.4430 (p) REVERT: B 93 THR cc_start: 0.8682 (m) cc_final: 0.8419 (p) REVERT: B 110 GLN cc_start: 0.8333 (mt0) cc_final: 0.8083 (mt0) REVERT: B 152 ILE cc_start: 0.8701 (tp) cc_final: 0.8461 (mt) REVERT: B 222 ARG cc_start: 0.6167 (mmm-85) cc_final: 0.5853 (mmm-85) REVERT: B 238 ASN cc_start: 0.7575 (t0) cc_final: 0.7309 (t0) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 0.1926 time to fit residues: 34.3805 Evaluate side-chains 140 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 56.4842 > 50: distance: 26 - 30: 28.722 distance: 30 - 31: 16.347 distance: 31 - 32: 18.196 distance: 31 - 34: 27.976 distance: 32 - 33: 18.452 distance: 32 - 38: 47.576 distance: 34 - 35: 20.187 distance: 35 - 36: 25.859 distance: 35 - 37: 5.698 distance: 38 - 39: 28.572 distance: 39 - 40: 23.568 distance: 39 - 42: 9.374 distance: 40 - 41: 21.735 distance: 40 - 46: 28.889 distance: 42 - 43: 22.169 distance: 43 - 44: 31.592 distance: 43 - 45: 26.646 distance: 46 - 47: 20.868 distance: 46 - 52: 21.771 distance: 47 - 48: 26.965 distance: 47 - 50: 25.860 distance: 48 - 49: 8.693 distance: 48 - 53: 20.270 distance: 50 - 51: 33.199 distance: 51 - 52: 40.723 distance: 53 - 54: 13.349 distance: 54 - 55: 12.034 distance: 54 - 57: 16.590 distance: 55 - 56: 37.772 distance: 55 - 61: 9.627 distance: 57 - 58: 16.375 distance: 58 - 59: 10.080 distance: 58 - 60: 9.239 distance: 61 - 62: 9.883 distance: 62 - 63: 20.020 distance: 62 - 65: 9.118 distance: 63 - 64: 20.296 distance: 63 - 73: 14.703 distance: 64 - 98: 40.677 distance: 65 - 66: 10.055 distance: 66 - 67: 14.185 distance: 66 - 68: 13.070 distance: 67 - 69: 9.676 distance: 68 - 70: 12.326 distance: 69 - 71: 7.459 distance: 70 - 71: 8.475 distance: 71 - 72: 9.901 distance: 73 - 74: 11.960 distance: 74 - 75: 11.659 distance: 74 - 77: 17.578 distance: 75 - 76: 16.536 distance: 75 - 82: 22.204 distance: 76 - 106: 41.210 distance: 77 - 78: 38.268 distance: 78 - 79: 11.968 distance: 79 - 80: 13.701 distance: 79 - 81: 21.842 distance: 82 - 83: 15.982 distance: 83 - 84: 15.557 distance: 84 - 85: 5.678 distance: 84 - 90: 8.478 distance: 86 - 87: 11.075 distance: 87 - 88: 17.439 distance: 87 - 89: 25.892 distance: 90 - 91: 11.600 distance: 91 - 94: 10.469 distance: 92 - 93: 14.668 distance: 92 - 98: 6.671 distance: 93 - 124: 26.269 distance: 94 - 95: 22.765 distance: 95 - 96: 34.348 distance: 95 - 97: 11.583 distance: 98 - 99: 7.834 distance: 99 - 100: 16.719 distance: 99 - 102: 19.587 distance: 100 - 101: 24.794 distance: 100 - 106: 29.316 distance: 102 - 103: 22.224 distance: 103 - 104: 4.629 distance: 103 - 105: 18.802 distance: 106 - 107: 23.793 distance: 107 - 108: 28.165 distance: 107 - 110: 19.749 distance: 108 - 109: 13.794 distance: 108 - 114: 11.935 distance: 110 - 111: 17.082 distance: 110 - 112: 13.142 distance: 111 - 113: 33.034