Starting phenix.real_space_refine on Thu Dec 7 20:16:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/12_2023/7y7w_33672_updated.pdb" } resolution = 2.4 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= 0.098 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2844 2.51 5 N 655 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4310 Unusual residues: {' CL': 1, ' NA': 2, 'ABU': 1, 'NAG': 3} Classifications: {'peptide': 529, 'undetermined': 7, 'water': 48} Link IDs: {'PTRANS': 22, 'TRANS': 506, None: 55} Not linked: pdbres="ILE A 577 " pdbres="ABU A 701 " Not linked: pdbres="ABU A 701 " pdbres="NAG A 702 " Not linked: pdbres="NAG A 702 " pdbres="NAG A 703 " Not linked: pdbres="NAG A 703 " pdbres="NAG A 704 " Not linked: pdbres="NAG A 704 " pdbres=" NA A 705 " ... (remaining 50 not shown) Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.69 Number of scatterers: 4310 At special positions: 0 Unit cell: (67.115, 72.5275, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 774 8.00 N 655 7.00 C 2844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.08 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 802.3 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.627A pdb=" N ILE A 84 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 154 removed outlier: 4.455A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 240 through 258 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.579A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.580A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 349 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 373 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 378 through 411 removed outlier: 3.720A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 438 removed outlier: 4.701A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.760A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 531 through 558 removed outlier: 4.996A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix removed outlier: 3.550A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.460A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 621 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: 1.12 Time building geometry restraints manager: 1.99 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: 620 1.29 - 1.42: 1312 1.42 - 1.55: 2407 1.55 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 4393 Sorted by residual: bond pdb=" C ASP A 395 " pdb=" O ASP A 395 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C PHE A 53 " pdb=" O PHE A 53 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.01e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.75e+00 ... (remaining 4388 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 90 105.83 - 112.88: 2238 112.88 - 119.94: 1636 119.94 - 127.00: 1946 127.00 - 134.06: 72 Bond angle restraints: 5982 Sorted by residual: angle pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.42 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 105.81 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 120.85 115.79 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.58 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 5977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2177 17.95 - 35.90: 257 35.90 - 53.86: 63 53.86 - 71.81: 15 71.81 - 89.76: 6 Dihedral angle restraints: 2518 sinusoidal: 995 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -49.63 -36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 663 0.277 - 0.554: 1 0.554 - 0.831: 0 0.831 - 1.108: 0 1.108 - 1.385: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 663 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.101 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" CG ASN A 181 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.307 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.134 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN A 184 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.203 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.064 2.00e-02 2.50e+03 6.39e-02 5.11e+01 pdb=" CG ASN A 176 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.077 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.10: 3270 3.10 - 3.70: 7039 3.70 - 4.30: 10496 4.30 - 4.90: 16729 Nonbonded interactions: 37574 Sorted by model distance: nonbonded pdb=" O HOH A 805 " pdb=" O HOH A 828 " model vdw 1.907 2.440 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 806 " model vdw 2.000 2.440 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 2.008 2.440 nonbonded pdb=" O LEU A 298 " pdb=" O HOH A 802 " model vdw 2.030 2.440 nonbonded pdb=" OG1 THR A 290 " pdb=" O HOH A 803 " model vdw 2.045 2.440 ... (remaining 37569 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: 0.460 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: 1.930 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.970 Find NCS groups from input model: 0.110 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:11.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 : 0.006 0.072 4393 Z= 0.358 Angle : 0.777 11.117 5982 Z= 0.474 Chirality : 0.084 1.385 666 Planarity : 0.005 0.042 725 Dihedral : 17.204 89.759 1549 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 26.73 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.36), residues: 527 helix: 0.63 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 500 HIS 0.007 0.002 HIS A 198 PHE 0.026 0.003 PHE A 398 TYR 0.020 0.002 TYR A 72 ARG 0.007 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.464 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.2117 time to fit residues: 81.8365 Evaluate side-chains 54 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4393 Z= 0.187 Angle : 0.588 8.829 5982 Z= 0.300 Chirality : 0.044 0.380 666 Planarity : 0.004 0.036 725 Dihedral : 6.481 59.170 639 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.23 % Allowed : 20.27 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.37), residues: 527 helix: 1.18 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 496 HIS 0.002 0.001 HIS A 198 PHE 0.030 0.002 PHE A 398 TYR 0.017 0.001 TYR A 72 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.497 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 73 average time/residue: 0.9818 time to fit residues: 75.1337 Evaluate side-chains 60 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.6651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 57 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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: 0.8261 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.176 Angle : 0.544 7.879 5982 Z= 0.281 Chirality : 0.044 0.328 666 Planarity : 0.004 0.032 725 Dihedral : 5.820 50.968 639 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.90 % Allowed : 20.49 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.37), residues: 527 helix: 1.29 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.36 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 496 HIS 0.001 0.001 HIS A 313 PHE 0.030 0.002 PHE A 398 TYR 0.014 0.001 TYR A 72 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.486 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 79 average time/residue: 0.9157 time to fit residues: 75.9631 Evaluate side-chains 74 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.0883 time to fit residues: 0.7652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 56 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.8289 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4393 Z= 0.203 Angle : 0.541 7.733 5982 Z= 0.286 Chirality : 0.044 0.273 666 Planarity : 0.004 0.034 725 Dihedral : 5.040 24.102 639 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.35 % Allowed : 20.71 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.37), residues: 527 helix: 1.33 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -1.39 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 116 HIS 0.001 0.001 HIS A 313 PHE 0.029 0.002 PHE A 398 TYR 0.017 0.002 TYR A 72 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 54 time to evaluate : 0.496 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 75 average time/residue: 0.8889 time to fit residues: 70.0584 Evaluate side-chains 68 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0847 time to fit residues: 0.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 52.941 > 50: distance: 27 - 32: 23.030 distance: 32 - 33: 18.303 distance: 33 - 34: 10.825 distance: 33 - 36: 16.155 distance: 34 - 35: 32.090 distance: 34 - 39: 15.751 distance: 36 - 37: 6.521 distance: 36 - 38: 12.296 distance: 39 - 40: 8.784 distance: 40 - 41: 18.539 distance: 40 - 43: 21.183 distance: 41 - 42: 34.629 distance: 41 - 47: 13.066 distance: 43 - 44: 16.864 distance: 44 - 45: 29.395 distance: 44 - 46: 20.205 distance: 47 - 48: 43.675 distance: 47 - 53: 23.827 distance: 48 - 49: 7.984 distance: 48 - 51: 24.447 distance: 49 - 50: 6.371 distance: 49 - 54: 37.538 distance: 51 - 52: 34.861 distance: 52 - 53: 8.464 distance: 55 - 56: 14.940 distance: 55 - 58: 18.206 distance: 56 - 57: 45.129 distance: 56 - 68: 10.645 distance: 58 - 59: 12.692 distance: 59 - 60: 16.469 distance: 59 - 61: 18.145 distance: 60 - 62: 3.680 distance: 61 - 63: 4.309 distance: 61 - 64: 6.085 distance: 62 - 63: 4.686 distance: 63 - 65: 3.262 distance: 64 - 66: 5.333 distance: 65 - 67: 6.916 distance: 66 - 67: 5.653 distance: 68 - 69: 14.558 distance: 69 - 70: 22.707 distance: 69 - 72: 12.002 distance: 70 - 71: 29.211 distance: 70 - 77: 20.681 distance: 72 - 73: 17.542 distance: 73 - 74: 28.812 distance: 74 - 75: 33.166 distance: 75 - 76: 36.952 distance: 77 - 78: 8.655 distance: 78 - 79: 16.088 distance: 78 - 81: 18.977 distance: 79 - 80: 16.768 distance: 79 - 86: 9.739 distance: 81 - 82: 18.724 distance: 82 - 83: 18.738 distance: 83 - 84: 27.182 distance: 83 - 85: 15.751 distance: 86 - 87: 31.356 distance: 87 - 88: 20.917 distance: 87 - 90: 17.141 distance: 88 - 89: 12.516 distance: 88 - 92: 12.835 distance: 90 - 91: 18.630 distance: 91 - 141: 13.020 distance: 92 - 93: 13.662 distance: 93 - 94: 18.348 distance: 93 - 96: 34.193 distance: 94 - 95: 16.126 distance: 94 - 100: 18.293 distance: 96 - 97: 26.501 distance: 97 - 98: 25.189 distance: 100 - 101: 4.045 distance: 101 - 102: 15.694 distance: 102 - 103: 20.572 distance: 102 - 108: 16.767 distance: 104 - 105: 4.125 distance: 105 - 106: 17.485 distance: 105 - 107: 17.260 distance: 108 - 109: 27.416 distance: 108 - 114: 22.026 distance: 109 - 110: 7.551 distance: 109 - 112: 34.221 distance: 110 - 115: 34.733 distance: 112 - 113: 14.907 distance: 113 - 114: 24.666