Starting phenix.real_space_refine on Tue Jan 14 15:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.map" model { file = "/net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qhp_18415/01_2025/8qhp_18415.cif" } resolution = 2.8 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= 0.010 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 Zn 2 6.06 5 S 22 5.16 5 C 4392 2.51 5 N 1128 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 236 SG CYS A 28 36.433 38.017 33.062 1.00137.77 S ATOM 1644 SG CYS A 208 33.883 39.740 30.430 1.00155.64 S ATOM 3629 SG CYS B 28 36.336 40.874 90.477 1.00138.97 S ATOM 5037 SG CYS B 208 37.721 38.524 92.922 1.00158.95 S Time building chain proxies: 4.56, per 1000 atoms: 0.67 Number of scatterers: 6788 At special positions: 0 Unit cell: (67.518, 71.148, 124.872, 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) Zn 2 29.99 S 22 16.00 O 1244 8.00 N 1128 7.00 C 4392 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: 1.63 Conformation dependent library (CDL) restraints added in 902.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 208 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 233 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 28 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 28 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 208 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 233 " 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 55.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 103 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.540A pdb=" N LEU A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.974A pdb=" N SER A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.679A pdb=" N PHE A 231 " --> pdb=" O ASP A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 304 through 329 Processing helix chain 'A' and resid 339 through 362 Processing helix chain 'A' and resid 365 through 387 Processing helix chain 'A' and resid 391 through 410 removed outlier: 3.502A pdb=" N LEU A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.715A pdb=" N GLU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.572A pdb=" N LEU B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.927A pdb=" N SER B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 304 through 332 removed outlier: 3.710A pdb=" N ARG B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 362 Processing helix chain 'B' and resid 365 through 387 Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65 removed outlier: 9.433A pdb=" N PHE A 220 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 24 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 254 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 223 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR A 256 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 225 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.453A pdb=" N ILE A 141 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 180 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65 removed outlier: 11.532A pdb=" N GLU B 22 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE B 222 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 24 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY B 224 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR B 26 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY B 226 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 221 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 254 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 223 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR B 256 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B 225 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.385A pdb=" N ILE B 141 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 180 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 363 hydrogen bonds defined for protein. 1071 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: 1.97 Time building geometry restraints manager: 1.82 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: 2164 1.34 - 1.46: 1623 1.46 - 1.58: 3137 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6962 Sorted by residual: bond pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 1.526 1.535 -0.008 9.00e-03 1.23e+04 8.57e-01 bond pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.18e-01 bond pdb=" CG1 ILE B 93 " pdb=" CD1 ILE B 93 " ideal model delta sigma weight residual 1.513 1.487 0.026 3.90e-02 6.57e+02 4.51e-01 bond pdb=" C ASP A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.336 1.342 -0.007 1.08e-02 8.57e+03 3.82e-01 ... (remaining 6957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 9020 0.85 - 1.70: 300 1.70 - 2.56: 23 2.56 - 3.41: 26 3.41 - 4.26: 1 Bond angle restraints: 9370 Sorted by residual: angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 106.21 110.47 -4.26 1.07e+00 8.73e-01 1.58e+01 angle pdb=" C VAL B 32 " pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta sigma weight residual 113.22 110.73 2.49 1.12e+00 7.97e-01 4.93e+00 angle pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" O VAL B 32 " ideal model delta sigma weight residual 122.63 120.99 1.64 8.70e-01 1.32e+00 3.56e+00 angle pdb=" CA TYR A 44 " pdb=" CB TYR A 44 " pdb=" CG TYR A 44 " ideal model delta sigma weight residual 113.90 111.19 2.71 1.80e+00 3.09e-01 2.27e+00 angle pdb=" CA TYR B 44 " pdb=" CB TYR B 44 " pdb=" CG TYR B 44 " ideal model delta sigma weight residual 113.90 111.31 2.59 1.80e+00 3.09e-01 2.07e+00 ... (remaining 9365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 3658 12.35 - 24.70: 347 24.70 - 37.05: 86 37.05 - 49.40: 34 49.40 - 61.75: 19 Dihedral angle restraints: 4144 sinusoidal: 1762 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LYS B 57 " pdb=" CB LYS B 57 " pdb=" CG LYS B 57 " pdb=" CD LYS B 57 " ideal model delta sinusoidal sigma weight residual -60.00 -119.56 59.56 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 295 " pdb=" CB LYS A 295 " pdb=" CG LYS A 295 " pdb=" CD LYS A 295 " ideal model delta sinusoidal sigma weight residual -60.00 -118.96 58.96 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 51 " pdb=" CB ARG A 51 " pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.05 -56.95 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 570 0.027 - 0.054: 237 0.054 - 0.082: 109 0.082 - 0.109: 33 0.109 - 0.136: 7 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA ILE B 141 " pdb=" N ILE B 141 " pdb=" C ILE B 141 " pdb=" CB ILE B 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA PHE A 92 " pdb=" N PHE A 92 " pdb=" C PHE A 92 " pdb=" CB PHE A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 953 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 195 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO A 196 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 201 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 202 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 148 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO B 149 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.015 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 235 2.72 - 3.27: 6703 3.27 - 3.81: 11579 3.81 - 4.36: 14304 4.36 - 4.90: 24475 Nonbonded interactions: 57296 Sorted by model distance: nonbonded pdb=" OE2 GLU B 237 " pdb="ZN ZN B 501 " model vdw 2.176 2.230 nonbonded pdb=" OG SER B 195 " pdb=" O GLY B 198 " model vdw 2.192 3.040 nonbonded pdb=" OE1 GLU B 286 " pdb=" OH TYR B 319 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 335 " pdb=" O ASP B 109 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP A 139 " pdb=" OH TYR A 142 " model vdw 2.219 3.040 ... (remaining 57291 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.640 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.050 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 0.026 6962 Z= 0.141 Angle : 0.384 4.260 9370 Z= 0.218 Chirality : 0.038 0.136 956 Planarity : 0.003 0.030 1202 Dihedral : 11.643 61.754 2624 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.77 (0.29), residues: 812 helix: 1.87 (0.25), residues: 424 sheet: 0.25 (0.53), residues: 84 loop : 0.61 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 249 HIS 0.001 0.000 HIS A 40 PHE 0.007 0.001 PHE B 356 TYR 0.010 0.001 TYR A 44 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.813 Fit side-chains REVERT: A 86 LYS cc_start: 0.8638 (tttt) cc_final: 0.8371 (tppt) REVERT: A 185 LYS cc_start: 0.9067 (mttt) cc_final: 0.8815 (mtmm) REVERT: A 199 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 76 LYS cc_start: 0.8952 (tppp) cc_final: 0.8701 (ttmm) REVERT: B 90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7956 (tm-30) REVERT: B 207 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7598 (pt0) REVERT: B 382 LYS cc_start: 0.8817 (tttt) cc_final: 0.8560 (tppp) REVERT: B 386 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8662 (mt-10) REVERT: B 414 ASP cc_start: 0.8827 (m-30) cc_final: 0.8347 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.4486 time to fit residues: 164.9207 Evaluate side-chains 78 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 11 GLN B 66 ASN B 233 HIS B 309 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.073377 restraints weight = 9835.639| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.86 r_work: 0.2640 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 6962 Z= 0.362 Angle : 0.513 11.467 9370 Z= 0.268 Chirality : 0.042 0.159 956 Planarity : 0.004 0.035 1202 Dihedral : 3.974 16.051 902 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.96 % Allowed : 8.80 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.89 (0.29), residues: 812 helix: 1.84 (0.24), residues: 442 sheet: 0.08 (0.50), residues: 92 loop : 0.92 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 249 HIS 0.003 0.001 HIS B 255 PHE 0.013 0.002 PHE A 92 TYR 0.018 0.001 TYR B 44 ARG 0.004 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8492 (tmm) REVERT: A 86 LYS cc_start: 0.8485 (tttt) cc_final: 0.8161 (tppt) REVERT: A 123 GLU cc_start: 0.9056 (tt0) cc_final: 0.8367 (tp30) REVERT: A 185 LYS cc_start: 0.9005 (mttt) cc_final: 0.8676 (mtmm) REVERT: A 199 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 90 GLU cc_start: 0.8468 (tt0) cc_final: 0.7954 (tm-30) outliers start: 14 outliers final: 3 residues processed: 91 average time/residue: 1.5322 time to fit residues: 145.7404 Evaluate side-chains 75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 56 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN B 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.076346 restraints weight = 9365.478| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.97 r_work: 0.2720 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6962 Z= 0.170 Angle : 0.444 12.385 9370 Z= 0.230 Chirality : 0.039 0.145 956 Planarity : 0.003 0.034 1202 Dihedral : 3.781 14.718 902 Min Nonbonded Distance : 1.553 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.54 % Allowed : 11.59 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.30), residues: 812 helix: 2.14 (0.25), residues: 442 sheet: -0.05 (0.49), residues: 92 loop : 1.06 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 204 HIS 0.021 0.001 HIS B 233 PHE 0.030 0.001 PHE A 273 TYR 0.013 0.001 TYR B 111 ARG 0.008 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8511 (tmm) REVERT: A 86 LYS cc_start: 0.8455 (tttt) cc_final: 0.8164 (tppt) REVERT: A 123 GLU cc_start: 0.9047 (tt0) cc_final: 0.8357 (tp30) REVERT: A 185 LYS cc_start: 0.9046 (mttt) cc_final: 0.8732 (mtmm) REVERT: A 199 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7979 (mt-10) REVERT: A 260 MET cc_start: 0.7962 (mmt) cc_final: 0.7241 (mmm) REVERT: A 266 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7698 (tpp) REVERT: B 71 ASP cc_start: 0.8537 (t0) cc_final: 0.8190 (t0) REVERT: B 90 GLU cc_start: 0.8447 (tt0) cc_final: 0.7905 (tm-30) outliers start: 11 outliers final: 4 residues processed: 90 average time/residue: 1.3994 time to fit residues: 132.3214 Evaluate side-chains 75 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 59.8738 > 50: distance: 64 - 69: 15.523 distance: 69 - 70: 27.106 distance: 69 - 75: 14.985 distance: 70 - 71: 18.940 distance: 70 - 73: 30.868 distance: 71 - 72: 18.876 distance: 71 - 76: 46.403 distance: 73 - 74: 37.651 distance: 74 - 75: 20.462 distance: 76 - 77: 41.702 distance: 77 - 78: 57.635 distance: 78 - 80: 49.677 distance: 80 - 81: 9.570 distance: 81 - 82: 13.584 distance: 81 - 84: 28.089 distance: 82 - 83: 4.170 distance: 82 - 89: 30.745 distance: 84 - 85: 27.439 distance: 85 - 86: 24.781 distance: 86 - 87: 18.454 distance: 86 - 88: 17.295 distance: 89 - 90: 40.110 distance: 89 - 95: 31.099 distance: 90 - 91: 33.704 distance: 90 - 93: 37.218 distance: 91 - 92: 13.328 distance: 91 - 96: 34.320 distance: 93 - 94: 6.760 distance: 94 - 95: 40.601 distance: 97 - 98: 24.766 distance: 97 - 100: 15.686 distance: 98 - 99: 14.539 distance: 98 - 105: 32.486 distance: 100 - 101: 43.077 distance: 101 - 102: 44.850 distance: 102 - 103: 17.824 distance: 103 - 104: 27.971 distance: 105 - 106: 12.903 distance: 106 - 107: 10.365 distance: 106 - 109: 23.988 distance: 107 - 108: 40.035 distance: 107 - 119: 26.736 distance: 109 - 110: 23.722 distance: 110 - 111: 32.162 distance: 110 - 112: 18.902 distance: 111 - 113: 5.874 distance: 112 - 114: 14.125 distance: 112 - 115: 10.848 distance: 113 - 114: 8.588 distance: 114 - 116: 9.948 distance: 115 - 117: 5.918 distance: 116 - 118: 15.109 distance: 117 - 118: 16.063 distance: 119 - 120: 23.702 distance: 120 - 121: 3.564 distance: 120 - 123: 20.426 distance: 121 - 122: 3.598 distance: 121 - 127: 11.711 distance: 123 - 124: 31.965 distance: 124 - 125: 31.837 distance: 124 - 126: 7.897 distance: 127 - 128: 40.815 distance: 128 - 129: 10.625 distance: 128 - 131: 22.609 distance: 129 - 130: 10.580 distance: 129 - 133: 24.250 distance: 131 - 132: 14.632 distance: 133 - 134: 21.148 distance: 133 - 139: 18.221 distance: 134 - 135: 16.486 distance: 134 - 137: 16.081 distance: 135 - 136: 6.640 distance: 135 - 140: 13.345 distance: 137 - 138: 24.549 distance: 138 - 139: 36.498 distance: 140 - 141: 3.394 distance: 141 - 142: 33.787 distance: 141 - 144: 4.558 distance: 142 - 143: 19.543 distance: 142 - 154: 20.305 distance: 144 - 145: 30.910 distance: 145 - 146: 21.927 distance: 145 - 147: 7.374 distance: 146 - 148: 9.321 distance: 147 - 149: 15.568 distance: 147 - 150: 11.404 distance: 148 - 149: 10.220 distance: 149 - 151: 9.105 distance: 150 - 152: 6.034 distance: 151 - 153: 16.098 distance: 152 - 153: 15.984