Starting phenix.real_space_refine on Fri Aug 2 18:22:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/08_2024/7p14_13155.cif" } resolution = 3.66 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= 0.002 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 25 5.16 5 C 2533 2.51 5 N 579 2.21 5 O 656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3796 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2706 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 126 Unusual residues: {'PLC': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 2.87, per 1000 atoms: 0.76 Number of scatterers: 3796 At special positions: 0 Unit cell: (96.348, 69.006, 70.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 3 15.00 O 656 8.00 N 579 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 631.7 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 67.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.515A pdb=" N ILE A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.741A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.762A pdb=" N GLY A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.530A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 158 removed outlier: 3.590A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Proline residue: A 145 - end of helix removed outlier: 3.572A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 removed outlier: 3.504A pdb=" N ARG A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 5.032A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 197 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 227 removed outlier: 3.654A pdb=" N LEU A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.535A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.733A pdb=" N PHE A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.233A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 Processing helix chain 'A' and resid 314 through 343 removed outlier: 3.616A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.778A pdb=" N TYR B 119 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.725A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 545 1.32 - 1.44: 1168 1.44 - 1.56: 2136 1.56 - 1.69: 6 1.69 - 1.81: 37 Bond restraints: 3892 Sorted by residual: bond pdb=" N LYS A 284 " pdb=" CA LYS A 284 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" C20 P5S A 403 " pdb=" C21 P5S A 403 " ideal model delta sigma weight residual 1.540 1.493 0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C4 PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.48e+00 bond pdb=" C4 PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 PLC A 402 " pdb=" O3P PLC A 402 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.69e+00 ... (remaining 3887 not shown) Histogram of bond angle deviations from ideal: 97.45 - 104.77: 39 104.77 - 112.09: 1914 112.09 - 119.40: 1221 119.40 - 126.72: 2040 126.72 - 134.04: 56 Bond angle restraints: 5270 Sorted by residual: angle pdb=" O3P PLC A 402 " pdb=" P PLC A 402 " pdb=" O4P PLC A 402 " ideal model delta sigma weight residual 93.62 104.20 -10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 103.08 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C3 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 107.38 114.66 -7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" CA LYS A 284 " pdb=" CB LYS A 284 " pdb=" CG LYS A 284 " ideal model delta sigma weight residual 114.10 118.68 -4.58 2.00e+00 2.50e-01 5.24e+00 angle pdb=" CA LEU A 330 " pdb=" CB LEU A 330 " pdb=" CG LEU A 330 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.65e+00 ... (remaining 5265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2099 27.26 - 54.52: 136 54.52 - 81.77: 21 81.77 - 109.03: 8 109.03 - 136.29: 3 Dihedral angle restraints: 2267 sinusoidal: 938 harmonic: 1329 Sorted by residual: dihedral pdb=" O2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 304.29 168.00 136.29 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" C3 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C2 PLC A 401 " pdb=" O3P PLC A 401 " ideal model delta sinusoidal sigma weight residual 67.16 -58.95 126.11 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C21 P5S A 403 " pdb=" C22 P5S A 403 " pdb=" C23 P5S A 403 " pdb=" C24 P5S A 403 " ideal model delta sinusoidal sigma weight residual 295.37 174.71 120.66 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 2264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 507 0.053 - 0.106: 73 0.106 - 0.159: 5 0.159 - 0.213: 0 0.213 - 0.266: 2 Chirality restraints: 587 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.05 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C2 P5S A 403 " pdb=" C1 P5S A 403 " pdb=" C3 P5S A 403 " pdb=" O37 P5S A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.33 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" C PRO A 201 " pdb=" CB PRO A 201 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 584 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 319 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 320 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 200 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 201 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 33 " -0.005 2.00e-02 2.50e+03 9.48e-03 8.99e-01 pdb=" C ASN B 33 " 0.016 2.00e-02 2.50e+03 pdb=" O ASN B 33 " -0.006 2.00e-02 2.50e+03 pdb=" N ILE B 34 " -0.005 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1090 2.82 - 3.34: 3666 3.34 - 3.86: 5942 3.86 - 4.38: 7105 4.38 - 4.90: 12065 Nonbonded interactions: 29868 Sorted by model distance: nonbonded pdb=" OE1 GLU A 260 " pdb=" NH2 ARG A 264 " model vdw 2.295 3.120 nonbonded pdb=" O ILE A 16 " pdb=" OG1 THR A 20 " model vdw 2.369 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O LEU A 371 " model vdw 2.372 3.040 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.393 3.040 nonbonded pdb=" OH TYR A 208 " pdb=" OH TYR A 291 " model vdw 2.419 3.040 ... (remaining 29863 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 18.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.004 0.047 3892 Z= 0.294 Angle : 0.627 10.583 5270 Z= 0.286 Chirality : 0.039 0.266 587 Planarity : 0.004 0.064 624 Dihedral : 19.089 136.288 1418 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.40), residues: 444 helix: 1.37 (0.31), residues: 257 sheet: 1.11 (0.70), residues: 52 loop : -0.55 (0.57), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 93 HIS 0.001 0.000 HIS A 56 PHE 0.005 0.001 PHE A 225 TYR 0.015 0.001 TYR A 340 ARG 0.002 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.460 Fit side-chains REVERT: A 139 THR cc_start: 0.9153 (m) cc_final: 0.8884 (p) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1404 time to fit residues: 13.0291 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3892 Z= 0.209 Angle : 0.603 9.719 5270 Z= 0.298 Chirality : 0.039 0.143 587 Planarity : 0.004 0.039 624 Dihedral : 18.301 129.435 623 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.01 % Allowed : 7.30 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.39), residues: 444 helix: 2.36 (0.29), residues: 265 sheet: 0.34 (0.69), residues: 57 loop : -0.41 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 93 HIS 0.002 0.001 HIS A 344 PHE 0.034 0.002 PHE A 94 TYR 0.015 0.001 TYR A 291 ARG 0.003 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.401 Fit side-chains REVERT: A 50 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7491 (m) REVERT: A 130 ASP cc_start: 0.8944 (t0) cc_final: 0.8720 (t70) REVERT: A 139 THR cc_start: 0.9138 (m) cc_final: 0.8829 (p) REVERT: A 252 GLN cc_start: 0.8284 (pm20) cc_final: 0.8037 (pt0) REVERT: B 127 GLN cc_start: 0.8569 (tp40) cc_final: 0.8305 (tp-100) outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.1330 time to fit residues: 12.7523 Evaluate side-chains 68 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 83 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3892 Z= 0.232 Angle : 0.573 9.242 5270 Z= 0.284 Chirality : 0.040 0.188 587 Planarity : 0.003 0.038 624 Dihedral : 17.719 128.522 623 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.52 % Allowed : 9.57 % Favored : 87.91 % 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: 2.41 (0.40), residues: 444 helix: 2.75 (0.29), residues: 264 sheet: 0.96 (0.69), residues: 52 loop : -0.66 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 245 HIS 0.001 0.001 HIS A 344 PHE 0.024 0.001 PHE A 104 TYR 0.020 0.001 TYR A 343 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.425 Fit side-chains REVERT: A 7 ASN cc_start: 0.8961 (t0) cc_final: 0.8693 (m-40) REVERT: A 130 ASP cc_start: 0.8932 (t0) cc_final: 0.8618 (t0) REVERT: A 137 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8632 (m-10) REVERT: A 232 LEU cc_start: 0.8407 (mp) cc_final: 0.8127 (mp) REVERT: A 258 SER cc_start: 0.8905 (t) cc_final: 0.8601 (p) REVERT: B 127 GLN cc_start: 0.8575 (tp40) cc_final: 0.8302 (tp-100) outliers start: 10 outliers final: 6 residues processed: 79 average time/residue: 0.1248 time to fit residues: 12.8615 Evaluate side-chains 77 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3892 Z= 0.222 Angle : 0.559 8.753 5270 Z= 0.276 Chirality : 0.040 0.196 587 Planarity : 0.003 0.032 624 Dihedral : 17.243 126.923 623 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.27 % Allowed : 11.84 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.40), residues: 444 helix: 2.93 (0.29), residues: 264 sheet: 0.86 (0.67), residues: 52 loop : -0.67 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 245 HIS 0.001 0.000 HIS A 250 PHE 0.012 0.001 PHE A 94 TYR 0.015 0.001 TYR B 121 ARG 0.002 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.400 Fit side-chains REVERT: A 130 ASP cc_start: 0.8767 (t0) cc_final: 0.8388 (t0) REVERT: A 137 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8656 (m-10) REVERT: A 258 SER cc_start: 0.8909 (t) cc_final: 0.8651 (p) REVERT: A 264 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7526 (ttm170) REVERT: B 127 GLN cc_start: 0.8540 (tp40) cc_final: 0.8251 (tp-100) outliers start: 9 outliers final: 4 residues processed: 74 average time/residue: 0.1604 time to fit residues: 15.1501 Evaluate side-chains 72 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 CYS Chi-restraints excluded: chain A residue 137 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.8322 > 50: distance: 39 - 44: 31.750 distance: 44 - 45: 10.952 distance: 45 - 46: 34.512 distance: 45 - 48: 39.769 distance: 46 - 47: 48.221 distance: 46 - 56: 46.611 distance: 48 - 49: 13.820 distance: 49 - 50: 10.133 distance: 49 - 51: 14.900 distance: 50 - 52: 15.055 distance: 51 - 53: 6.520 distance: 52 - 54: 4.495 distance: 56 - 57: 39.941 distance: 57 - 58: 38.211 distance: 57 - 60: 20.431 distance: 58 - 59: 33.697 distance: 58 - 68: 28.049 distance: 60 - 61: 12.084 distance: 61 - 62: 43.594 distance: 61 - 63: 40.382 distance: 62 - 64: 18.349 distance: 63 - 65: 40.240 distance: 64 - 66: 28.055 distance: 65 - 66: 4.023 distance: 66 - 67: 38.265 distance: 68 - 69: 34.201 distance: 69 - 70: 18.942 distance: 69 - 72: 3.550 distance: 70 - 71: 11.109 distance: 70 - 73: 24.825 distance: 73 - 74: 41.852 distance: 74 - 77: 42.563 distance: 75 - 76: 40.244 distance: 75 - 81: 27.099 distance: 77 - 78: 26.477 distance: 78 - 79: 19.972 distance: 78 - 80: 16.792 distance: 81 - 82: 43.470 distance: 82 - 83: 33.882 distance: 82 - 85: 19.020 distance: 83 - 84: 19.216 distance: 85 - 86: 34.911 distance: 87 - 88: 5.231 distance: 88 - 89: 48.826 distance: 88 - 91: 30.929 distance: 89 - 90: 51.077 distance: 89 - 94: 31.003 distance: 91 - 92: 16.182 distance: 91 - 93: 35.454 distance: 94 - 95: 13.443 distance: 95 - 96: 43.154 distance: 95 - 98: 48.896 distance: 96 - 97: 39.224 distance: 96 - 103: 20.837 distance: 98 - 99: 31.571 distance: 99 - 100: 43.010 distance: 100 - 101: 27.053 distance: 101 - 102: 27.632 distance: 103 - 104: 32.691 distance: 104 - 105: 42.804 distance: 105 - 106: 31.878 distance: 105 - 107: 7.448 distance: 107 - 108: 6.885 distance: 108 - 109: 45.733 distance: 108 - 111: 31.358 distance: 109 - 110: 20.304 distance: 109 - 118: 37.195 distance: 111 - 112: 39.051 distance: 113 - 114: 49.802 distance: 114 - 115: 15.014 distance: 115 - 116: 42.699 distance: 115 - 117: 45.625 distance: 118 - 119: 6.041 distance: 119 - 120: 53.222 distance: 119 - 122: 28.136 distance: 120 - 121: 3.348 distance: 120 - 129: 32.252 distance: 122 - 123: 49.219 distance: 123 - 124: 58.306 distance: 123 - 125: 40.109 distance: 124 - 126: 27.721 distance: 125 - 127: 37.425 distance: 126 - 128: 17.755 distance: 127 - 128: 26.261