Starting phenix.real_space_refine on Thu Jul 18 22:58:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hff_34719/07_2024/8hff_34719.cif" } resolution = 2.86 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= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2953 2.51 5 N 681 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 371": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4399 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4373 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Unusual residues: {'LNR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 2.88, per 1000 atoms: 0.65 Number of scatterers: 4399 At special positions: 0 Unit cell: (70.3625, 69.28, 98.5075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 745 8.00 N 681 7.00 C 2953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " 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: 2.02 Conformation dependent library (CDL) restraints added in 797.8 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 1 sheets defined 82.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.649A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.691A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 130 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.639A pdb=" N THR A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 261 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 283 removed outlier: 3.817A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.906A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.714A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 305 through 319 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.968A pdb=" N TYR A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 385 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.615A pdb=" N TRP A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.796A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 497 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.587A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.507A pdb=" N ILE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 604 removed outlier: 4.040A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.759A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545 302 hydrogen bonds defined for protein. 867 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: 1.14 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 649 1.29 - 1.42: 1370 1.42 - 1.55: 2488 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4538 Sorted by residual: bond pdb=" C GLY A 92 " pdb=" O GLY A 92 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.35e-02 5.49e+03 2.98e+01 bond pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 1.232 1.167 0.065 1.36e-02 5.41e+03 2.31e+01 bond pdb=" C GLY A 92 " pdb=" N ALA A 93 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.40e-02 5.10e+03 2.09e+01 bond pdb=" C GLY A 91 " pdb=" O GLY A 91 " ideal model delta sigma weight residual 1.235 1.186 0.048 1.35e-02 5.49e+03 1.28e+01 bond pdb=" C GLY A 90 " pdb=" O GLY A 90 " ideal model delta sigma weight residual 1.235 1.191 0.043 1.35e-02 5.49e+03 1.03e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 134 107.24 - 113.92: 2497 113.92 - 120.60: 1976 120.60 - 127.28: 1517 127.28 - 133.96: 66 Bond angle restraints: 6190 Sorted by residual: angle pdb=" CA ASN A 89 " pdb=" C ASN A 89 " pdb=" O ASN A 89 " ideal model delta sigma weight residual 121.17 117.39 3.78 1.24e+00 6.50e-01 9.29e+00 angle pdb=" N GLY A 90 " pdb=" CA GLY A 90 " pdb=" C GLY A 90 " ideal model delta sigma weight residual 113.18 119.71 -6.53 2.37e+00 1.78e-01 7.59e+00 angle pdb=" C ASN A 89 " pdb=" CA ASN A 89 " pdb=" CB ASN A 89 " ideal model delta sigma weight residual 111.23 115.90 -4.67 1.70e+00 3.46e-01 7.53e+00 angle pdb=" C PHE A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 121.14 116.53 4.61 1.75e+00 3.27e-01 6.93e+00 angle pdb=" CA TYR A 151 " pdb=" CB TYR A 151 " pdb=" CG TYR A 151 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.59e+00 ... (remaining 6185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 2209 17.79 - 35.58: 251 35.58 - 53.37: 61 53.37 - 71.16: 15 71.16 - 88.95: 1 Dihedral angle restraints: 2537 sinusoidal: 957 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ILE A 103 " pdb=" C ILE A 103 " pdb=" N ILE A 104 " pdb=" CA ILE A 104 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" C TYR A 205 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual -122.60 -131.34 8.74 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" CA ASP A 64 " pdb=" CB ASP A 64 " pdb=" CG ASP A 64 " pdb=" OD1 ASP A 64 " ideal model delta sinusoidal sigma weight residual -30.00 -89.91 59.91 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 633 0.067 - 0.135: 54 0.135 - 0.202: 3 0.202 - 0.270: 0 0.270 - 0.337: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA TYR A 205 " pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CB TYR A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CAL LNR A 702 " pdb=" CAH LNR A 702 " pdb=" CAK LNR A 702 " pdb=" OAD LNR A 702 " both_signs ideal model delta sigma weight residual False -2.28 -2.43 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 688 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C ILE A 103 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " -0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ASN A 89 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN A 89 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 90 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 88 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C LYS A 88 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS A 88 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 89 " 0.017 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 79 2.69 - 3.25: 4446 3.25 - 3.80: 7147 3.80 - 4.35: 9270 4.35 - 4.90: 16096 Nonbonded interactions: 37038 Sorted by model distance: nonbonded pdb=" OD1 ASP A 75 " pdb=" OG SER A 419 " model vdw 2.142 2.440 nonbonded pdb=" O ALA A 328 " pdb=" OG SER A 331 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASN A 337 " pdb=" N ASN A 338 " model vdw 2.287 2.520 nonbonded pdb=" O THR A 283 " pdb=" OG1 THR A 283 " model vdw 2.327 2.440 nonbonded pdb=" N ASP A 175 " pdb=" OD1 ASP A 175 " model vdw 2.367 2.520 ... (remaining 37033 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 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: 0.420 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 0.074 4538 Z= 0.236 Angle : 0.544 6.527 6190 Z= 0.292 Chirality : 0.040 0.337 691 Planarity : 0.004 0.039 751 Dihedral : 16.022 88.952 1528 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.39 % 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: 1.96 (0.38), residues: 543 helix: 1.68 (0.28), residues: 376 sheet: None (None), residues: 0 loop : 0.60 (0.53), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.001 0.000 HIS A 296 PHE 0.009 0.001 PHE A 362 TYR 0.018 0.001 TYR A 151 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.7220 time to fit residues: 43.8980 Evaluate side-chains 54 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 498 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4538 Z= 0.204 Angle : 0.512 7.501 6190 Z= 0.266 Chirality : 0.040 0.147 691 Planarity : 0.004 0.047 751 Dihedral : 5.773 58.229 607 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.17 % Allowed : 17.14 % Favored : 80.69 % 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: 2.04 (0.38), residues: 543 helix: 1.78 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.48 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 370 PHE 0.016 0.001 PHE A 101 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8065 (m-80) cc_final: 0.7726 (m-10) REVERT: A 459 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 506 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7410 (tm-30) outliers start: 10 outliers final: 3 residues processed: 56 average time/residue: 0.5973 time to fit residues: 36.1030 Evaluate side-chains 50 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4538 Z= 0.301 Angle : 0.550 8.853 6190 Z= 0.288 Chirality : 0.042 0.162 691 Planarity : 0.004 0.049 751 Dihedral : 5.344 52.428 602 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.47 % Allowed : 15.62 % Favored : 80.91 % 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: 1.76 (0.37), residues: 543 helix: 1.54 (0.27), residues: 383 sheet: None (None), residues: 0 loop : 0.44 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 253 HIS 0.002 0.000 HIS A 280 PHE 0.013 0.002 PHE A 316 TYR 0.022 0.001 TYR A 84 ARG 0.001 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 42 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8068 (m-80) cc_final: 0.7742 (m-10) REVERT: A 365 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6741 (pt) REVERT: A 459 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6870 (t80) REVERT: A 509 MET cc_start: 0.8385 (mtp) cc_final: 0.7803 (mtm) outliers start: 16 outliers final: 5 residues processed: 53 average time/residue: 0.6491 time to fit residues: 37.1902 Evaluate side-chains 46 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 547 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.0470 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4538 Z= 0.170 Angle : 0.476 6.635 6190 Z= 0.251 Chirality : 0.038 0.144 691 Planarity : 0.004 0.050 751 Dihedral : 4.700 47.817 602 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.39 % Allowed : 17.14 % Favored : 80.48 % 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: 2.06 (0.37), residues: 543 helix: 1.79 (0.27), residues: 384 sheet: None (None), residues: 0 loop : 0.49 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 553 HIS 0.001 0.000 HIS A 280 PHE 0.012 0.001 PHE A 110 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8066 (m-80) cc_final: 0.7721 (m-10) REVERT: A 459 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 509 MET cc_start: 0.8358 (mtp) cc_final: 0.7834 (mtm) outliers start: 11 outliers final: 4 residues processed: 54 average time/residue: 0.6290 time to fit residues: 36.6001 Evaluate side-chains 50 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 547 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6852 > 50: distance: 68 - 73: 3.257 distance: 75 - 80: 34.085 distance: 81 - 82: 11.974 distance: 82 - 83: 27.417 distance: 82 - 91: 49.948 distance: 84 - 85: 13.491 distance: 85 - 86: 12.057 distance: 85 - 87: 25.623 distance: 86 - 88: 47.048 distance: 87 - 89: 11.096 distance: 88 - 90: 57.489 distance: 89 - 90: 13.753 distance: 92 - 93: 40.523 distance: 92 - 95: 57.276 distance: 93 - 94: 48.199 distance: 97 - 98: 48.092 distance: 98 - 99: 31.109 distance: 100 - 106: 57.003 distance: 101 - 102: 60.557 distance: 101 - 104: 55.851 distance: 102 - 103: 15.288 distance: 102 - 107: 46.945 distance: 104 - 105: 40.830 distance: 105 - 106: 39.171 distance: 107 - 108: 31.903 distance: 108 - 109: 17.111 distance: 108 - 111: 30.342 distance: 109 - 110: 24.007 distance: 109 - 115: 17.276 distance: 111 - 112: 40.925 distance: 112 - 113: 68.059 distance: 112 - 114: 54.956 distance: 116 - 117: 38.532 distance: 116 - 119: 28.411 distance: 117 - 122: 57.057 distance: 119 - 120: 45.989 distance: 119 - 121: 42.968 distance: 122 - 123: 39.685 distance: 122 - 153: 69.195 distance: 123 - 124: 41.452 distance: 124 - 125: 39.195 distance: 125 - 150: 37.572 distance: 126 - 127: 41.834 distance: 127 - 128: 31.240 distance: 127 - 129: 9.645 distance: 130 - 132: 39.608 distance: 131 - 132: 56.464 distance: 132 - 133: 40.444 distance: 134 - 135: 4.657 distance: 135 - 136: 33.840 distance: 135 - 138: 33.355 distance: 136 - 137: 39.648 distance: 136 - 142: 40.287 distance: 138 - 139: 44.578 distance: 139 - 140: 19.205 distance: 139 - 141: 19.904 distance: 142 - 143: 39.856 distance: 143 - 144: 29.810 distance: 143 - 146: 41.053 distance: 144 - 145: 41.595 distance: 144 - 150: 49.980 distance: 146 - 147: 39.967 distance: 147 - 148: 40.014 distance: 151 - 152: 32.127 distance: 151 - 154: 40.146 distance: 152 - 153: 50.408 distance: 152 - 162: 7.654 distance: 155 - 157: 22.934 distance: 156 - 158: 14.494 distance: 157 - 159: 18.589 distance: 158 - 160: 13.476 distance: 159 - 160: 39.533 distance: 163 - 164: 33.517 distance: 164 - 165: 35.867 distance: 164 - 170: 31.963