Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 01:26:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/04_2023/7p14_13155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/04_2023/7p14_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_13155/04_2023/7p14_13155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/04_2023/7p14_13155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/04_2023/7p14_13155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p14_13155/04_2023/7p14_13155_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 2.75, per 1000 atoms: 0.72 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: 1.86 Conformation dependent library (CDL) restraints added in 559.3 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... running ksdssp... Secondary structure from input PDB file: 15 helices and 2 sheets defined 61.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 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 38 through 66 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 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 88 through 104 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 157 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 162 through 189 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 196 removed outlier: 5.032A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 226 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 228 through 249 Processing helix chain 'A' and resid 257 through 273 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 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 285 through 307 Processing helix chain 'A' and resid 315 through 342 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 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing sheet with id= A, first strand: chain 'B' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 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) 233 hydrogen bonds defined for protein. 678 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: 1.01 Time building geometry restraints manager: 1.97 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=" C3 P5S A 403 " pdb=" O16 P5S A 403 " ideal model delta sigma weight residual 1.405 1.456 -0.051 2.00e-02 2.50e+03 6.38e+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 - 22.82: 2014 22.82 - 45.64: 172 45.64 - 68.45: 19 68.45 - 91.27: 9 91.27 - 114.09: 2 Dihedral angle restraints: 2216 sinusoidal: 887 harmonic: 1329 Sorted by residual: dihedral pdb=" C27 P5S A 403 " pdb=" C28 P5S A 403 " pdb=" C29 P5S A 403 " pdb=" C30 P5S A 403 " ideal model delta sinusoidal sigma weight residual -179.38 -65.29 -114.09 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA ILE A 319 " pdb=" C ILE A 319 " pdb=" N PRO A 320 " pdb=" CA PRO A 320 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" C41 P5S A 403 " pdb=" C42 P5S A 403 " pdb=" C43 P5S A 403 " pdb=" C44 P5S A 403 " ideal model delta sinusoidal sigma weight residual 181.47 89.64 91.83 1 3.00e+01 1.11e-03 1.10e+01 ... (remaining 2213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 508 0.053 - 0.106: 74 0.106 - 0.159: 4 0.159 - 0.213: 0 0.213 - 0.266: 1 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=" 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 chirality pdb=" CA PHE A 276 " pdb=" N PHE A 276 " pdb=" C PHE A 276 " pdb=" CB PHE A 276 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-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: 1091 2.82 - 3.34: 3686 3.34 - 3.86: 5967 3.86 - 4.38: 7145 4.38 - 4.90: 12071 Nonbonded interactions: 29960 Sorted by model distance: nonbonded pdb=" OE1 GLU A 260 " pdb=" NH2 ARG A 264 " model vdw 2.295 2.520 nonbonded pdb=" O ILE A 16 " pdb=" OG1 THR A 20 " model vdw 2.369 2.440 nonbonded pdb=" OH TYR A 182 " pdb=" O LEU A 371 " model vdw 2.372 2.440 nonbonded pdb=" O ILE A 175 " pdb=" OG1 THR A 179 " model vdw 2.393 2.440 nonbonded pdb=" OH TYR A 208 " pdb=" OH TYR A 291 " model vdw 2.419 2.440 ... (remaining 29955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.590 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.280 Find NCS groups from input model: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- 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 0.051 3892 Z= 0.305 Angle : 0.638 10.583 5270 Z= 0.289 Chirality : 0.037 0.266 587 Planarity : 0.004 0.064 624 Dihedral : 16.559 114.091 1367 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 % 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 *********************** 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 : 0.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1745 time to fit residues: 16.0172 Evaluate side-chains 62 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5185 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.0060 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3892 Z= 0.187 Angle : 0.553 6.488 5270 Z= 0.279 Chirality : 0.038 0.126 587 Planarity : 0.004 0.040 624 Dihedral : 12.334 77.717 572 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.02 % 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: 2.12 (0.39), residues: 444 helix: 2.48 (0.30), residues: 257 sheet: 1.02 (0.69), residues: 52 loop : -0.60 (0.57), residues: 135 *********************** 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 78 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.437 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 75 average time/residue: 0.1372 time to fit residues: 13.3881 Evaluate side-chains 67 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0399 time to fit residues: 0.8896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3892 Z= 0.197 Angle : 0.516 5.737 5270 Z= 0.258 Chirality : 0.038 0.171 587 Planarity : 0.003 0.032 624 Dihedral : 10.432 73.756 572 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.76 % 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: 2.50 (0.39), residues: 444 helix: 2.87 (0.29), residues: 260 sheet: 1.04 (0.69), residues: 52 loop : -0.68 (0.56), residues: 132 *********************** 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 75 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.456 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1408 time to fit residues: 12.8847 Evaluate side-chains 67 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0384 time to fit residues: 0.9261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3892 Z= 0.208 Angle : 0.518 5.999 5270 Z= 0.261 Chirality : 0.038 0.173 587 Planarity : 0.003 0.030 624 Dihedral : 9.708 73.360 572 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 2.27 % 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: 2.62 (0.40), residues: 444 helix: 3.05 (0.29), residues: 260 sheet: 0.98 (0.69), residues: 52 loop : -0.76 (0.56), residues: 132 *********************** 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 70 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.452 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 0.1504 time to fit residues: 13.0886 Evaluate side-chains 61 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0391 time to fit residues: 0.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3892 Z= 0.184 Angle : 0.503 5.801 5270 Z= 0.254 Chirality : 0.037 0.177 587 Planarity : 0.003 0.026 624 Dihedral : 9.118 72.837 572 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.76 % 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: 2.75 (0.40), residues: 444 helix: 3.17 (0.29), residues: 260 sheet: 1.00 (0.68), residues: 52 loop : -0.74 (0.56), residues: 132 *********************** REFINEMENT MACRO_CYCLE 5 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: 7 poor density : 65 time to evaluate : 0.430 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.1345 time to fit residues: 11.9742 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0371 time to fit residues: 0.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3892 Z= 0.216 Angle : 0.532 6.400 5270 Z= 0.264 Chirality : 0.038 0.184 587 Planarity : 0.003 0.024 624 Dihedral : 8.899 72.957 572 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.39), residues: 444 helix: 3.10 (0.29), residues: 260 sheet: 0.99 (0.67), residues: 52 loop : -0.75 (0.56), residues: 132 *********************** REFINEMENT MACRO_CYCLE 6 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 69 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.1512 time to fit residues: 12.9076 Evaluate side-chains 63 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0411 time to fit residues: 0.7963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 72.3584 > 50: distance: 15 - 37: 37.205 distance: 30 - 56: 32.993 distance: 34 - 37: 33.907 distance: 35 - 65: 32.468 distance: 37 - 38: 55.882 distance: 38 - 39: 40.480 distance: 38 - 41: 55.908 distance: 39 - 45: 69.883 distance: 41 - 42: 40.029 distance: 42 - 43: 56.389 distance: 42 - 44: 38.903 distance: 45 - 46: 40.060 distance: 46 - 47: 38.936 distance: 46 - 49: 69.911 distance: 47 - 48: 56.311 distance: 47 - 56: 39.760 distance: 50 - 51: 55.460 distance: 51 - 52: 39.879 distance: 52 - 53: 40.899 distance: 53 - 54: 40.490 distance: 56 - 57: 39.429 distance: 57 - 58: 39.425 distance: 57 - 60: 40.472 distance: 58 - 59: 41.097 distance: 58 - 65: 57.406 distance: 60 - 61: 58.020 distance: 63 - 64: 57.281 distance: 66 - 67: 57.294 distance: 66 - 69: 40.333 distance: 67 - 68: 40.539 distance: 67 - 71: 40.201 distance: 69 - 70: 39.158 distance: 71 - 72: 55.446 distance: 72 - 75: 40.751 distance: 73 - 74: 41.022 distance: 73 - 79: 55.241 distance: 75 - 76: 57.728 distance: 76 - 77: 40.351 distance: 76 - 78: 39.270 distance: 79 - 85: 56.601 distance: 80 - 83: 57.396 distance: 81 - 86: 39.908 distance: 82 - 103: 57.213 distance: 83 - 84: 39.588 distance: 84 - 85: 40.477 distance: 87 - 88: 56.520 distance: 87 - 90: 40.021 distance: 88 - 89: 56.686 distance: 90 - 91: 40.542 distance: 91 - 92: 56.332 distance: 91 - 93: 56.287 distance: 95 - 96: 40.346 distance: 96 - 97: 40.423 distance: 96 - 103: 56.189 distance: 97 - 119: 34.273 distance: 98 - 99: 56.175 distance: 99 - 100: 70.219 distance: 100 - 101: 69.546 distance: 101 - 102: 55.902 distance: 104 - 105: 39.794 distance: 104 - 107: 38.965 distance: 105 - 111: 56.871 distance: 108 - 109: 68.782 distance: 108 - 110: 57.726 distance: 111 - 112: 40.610 distance: 113 - 119: 34.131 distance: 116 - 117: 39.447 distance: 116 - 118: 40.000