Starting phenix.real_space_refine on Fri Aug 2 18:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfi_34721/08_2024/8hfi_34721.cif" } resolution = 2.5 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= 0.144 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 S 20 5.16 5 Cl 1 4.86 5 C 2963 2.51 5 N 681 2.21 5 O 778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 488": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4443 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4383 Classifications: {'peptide': 548} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 60 Unusual residues: {' CL': 1, 'DSM': 1} Classifications: {'undetermined': 2, 'water': 39} Link IDs: {None: 40} Time building chain proxies: 3.19, per 1000 atoms: 0.72 Number of scatterers: 4443 At special positions: 0 Unit cell: (69.28, 68.1975, 97.425, 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) Cl 1 17.00 S 20 16.00 O 778 8.00 N 681 7.00 C 2963 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: 2.03 Conformation dependent library (CDL) restraints added in 731.5 milliseconds 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 83.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.552A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.518A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.256A 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 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' 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: 3.623A pdb=" N TRP A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.716A 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 removed outlier: 3.520A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) 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 262 through 283 removed outlier: 3.854A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.826A pdb=" N THR A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.767A pdb=" N GLU A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 373 Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.798A pdb=" N VAL A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Proline residue: A 392 - end of helix removed outlier: 3.705A pdb=" N THR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.659A pdb=" N GLY A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.613A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 496 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: 3.594A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 592 Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.790A pdb=" N HIS A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS A 599 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 602 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.813A 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 545 299 hydrogen bonds defined for protein. 855 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: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 647 1.30 - 1.43: 1376 1.43 - 1.55: 2493 1.55 - 1.68: 0 1.68 - 1.81: 31 Bond restraints: 4547 Sorted by residual: bond pdb=" C SER A 318 " pdb=" O SER A 318 " ideal model delta sigma weight residual 1.236 1.167 0.070 1.15e-02 7.56e+03 3.70e+01 bond pdb=" CA SER A 318 " pdb=" CB SER A 318 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.55e-02 4.16e+03 2.13e+01 bond pdb=" N GLY A 60 " pdb=" CA GLY A 60 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" C5 DSM A 701 " pdb=" C6 DSM A 701 " ideal model delta sigma weight residual 1.524 1.549 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" CG1 ILE A 481 " pdb=" CD1 ILE A 481 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.38e+00 ... (remaining 4542 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.23: 144 107.23 - 113.92: 2498 113.92 - 120.61: 1972 120.61 - 127.30: 1519 127.30 - 133.99: 69 Bond angle restraints: 6202 Sorted by residual: angle pdb=" C PHE A 317 " pdb=" N SER A 318 " pdb=" CA SER A 318 " ideal model delta sigma weight residual 120.44 127.79 -7.35 1.30e+00 5.92e-01 3.20e+01 angle pdb=" CA SER A 318 " pdb=" C SER A 318 " pdb=" O SER A 318 " ideal model delta sigma weight residual 120.82 116.52 4.30 1.05e+00 9.07e-01 1.67e+01 angle pdb=" C GLY A 106 " pdb=" N MET A 107 " pdb=" CA MET A 107 " ideal model delta sigma weight residual 119.78 114.75 5.03 1.24e+00 6.50e-01 1.64e+01 angle pdb=" N TYR A 205 " pdb=" CA TYR A 205 " pdb=" C TYR A 205 " ideal model delta sigma weight residual 110.80 118.44 -7.64 2.13e+00 2.20e-01 1.29e+01 angle pdb=" C4 DSM A 701 " pdb=" C13 DSM A 701 " pdb=" C5 DSM A 701 " ideal model delta sigma weight residual 115.54 125.95 -10.41 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 2242 17.44 - 34.87: 216 34.87 - 52.31: 65 52.31 - 69.74: 14 69.74 - 87.18: 2 Dihedral angle restraints: 2539 sinusoidal: 955 harmonic: 1584 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 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+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 -132.79 10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" N TYR A 205 " pdb=" C TYR A 205 " pdb=" CA TYR A 205 " pdb=" CB TYR A 205 " ideal model delta harmonic sigma weight residual 122.80 132.66 -9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 2536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 670 0.091 - 0.181: 19 0.181 - 0.271: 0 0.271 - 0.362: 0 0.362 - 0.452: 1 Chirality restraints: 690 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 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 687 not shown) Planarity restraints: 752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 103 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ILE A 103 " -0.070 2.00e-02 2.50e+03 pdb=" O ILE A 103 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 104 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 318 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C SER A 318 " -0.058 2.00e-02 2.50e+03 pdb=" O SER A 318 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A 319 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DSM A 701 " -0.013 2.00e-02 2.50e+03 2.22e-02 9.86e+00 pdb=" C13 DSM A 701 " 0.010 2.00e-02 2.50e+03 pdb=" C14 DSM A 701 " -0.041 2.00e-02 2.50e+03 pdb=" C2 DSM A 701 " -0.000 2.00e-02 2.50e+03 pdb=" C3 DSM A 701 " 0.017 2.00e-02 2.50e+03 pdb=" C4 DSM A 701 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DSM A 701 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DSM A 701 " 0.038 2.00e-02 2.50e+03 ... (remaining 749 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 33 2.59 - 3.16: 3814 3.16 - 3.74: 7288 3.74 - 4.32: 10368 4.32 - 4.90: 17016 Nonbonded interactions: 38519 Sorted by model distance: nonbonded pdb=" O HOH A 808 " pdb=" O HOH A 838 " model vdw 2.008 3.040 nonbonded pdb=" O HOH A 812 " pdb=" O HOH A 821 " model vdw 2.045 3.040 nonbonded pdb=" O PHE A 475 " pdb=" O HOH A 801 " model vdw 2.089 3.040 nonbonded pdb=" O ALA A 589 " pdb=" OG1 THR A 593 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" O HOH A 802 " model vdw 2.180 3.040 ... (remaining 38514 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: 0.330 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.040 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:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.003 0.072 4547 Z= 0.223 Angle : 0.628 10.413 6202 Z= 0.331 Chirality : 0.041 0.452 690 Planarity : 0.004 0.041 752 Dihedral : 15.560 87.178 1528 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.08 % Allowed : 16.23 % Favored : 82.68 % 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: 1.51 (0.38), residues: 544 helix: 1.42 (0.28), residues: 375 sheet: None (None), residues: 0 loop : 0.22 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 80 HIS 0.001 0.000 HIS A 220 PHE 0.011 0.001 PHE A 409 TYR 0.013 0.001 TYR A 84 ARG 0.001 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.458 Fit side-chains REVERT: A 488 GLU cc_start: 0.8457 (tt0) cc_final: 0.8223 (tt0) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.8462 time to fit residues: 53.6830 Evaluate side-chains 56 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 396 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 375 ASN A 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4547 Z= 0.256 Angle : 0.623 8.572 6202 Z= 0.312 Chirality : 0.043 0.143 690 Planarity : 0.005 0.042 752 Dihedral : 7.519 61.121 605 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.95 % Allowed : 14.29 % Favored : 83.77 % 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: 1.49 (0.37), residues: 544 helix: 1.28 (0.27), residues: 387 sheet: None (None), residues: 0 loop : 0.49 (0.55), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.002 0.001 HIS A 220 PHE 0.013 0.002 PHE A 409 TYR 0.015 0.001 TYR A 84 ARG 0.002 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.504 Fit side-chains REVERT: A 242 MET cc_start: 0.8616 (mtp) cc_final: 0.8307 (mtp) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.7262 time to fit residues: 45.0321 Evaluate side-chains 57 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 450 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS A 375 ASN A 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4547 Z= 0.175 Angle : 0.552 8.263 6202 Z= 0.274 Chirality : 0.040 0.132 690 Planarity : 0.004 0.038 752 Dihedral : 7.328 63.886 602 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.73 % Allowed : 15.37 % Favored : 82.90 % 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: 1.81 (0.37), residues: 544 helix: 1.59 (0.27), residues: 382 sheet: None (None), residues: 0 loop : 0.45 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.011 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.504 Fit side-chains REVERT: A 488 GLU cc_start: 0.8365 (tt0) cc_final: 0.8121 (tt0) REVERT: A 515 LEU cc_start: 0.8949 (tp) cc_final: 0.8709 (tp) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.7054 time to fit residues: 46.7533 Evaluate side-chains 58 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 ASN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4547 Z= 0.178 Angle : 0.552 8.284 6202 Z= 0.273 Chirality : 0.040 0.131 690 Planarity : 0.004 0.037 752 Dihedral : 7.037 63.694 600 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.16 % Allowed : 15.58 % Favored : 82.25 % 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: 1.80 (0.37), residues: 544 helix: 1.57 (0.26), residues: 386 sheet: None (None), residues: 0 loop : 0.45 (0.54), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.002 0.001 HIS A 280 PHE 0.012 0.001 PHE A 409 TYR 0.016 0.001 TYR A 84 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.438 Fit side-chains REVERT: A 242 MET cc_start: 0.8608 (mtp) cc_final: 0.8356 (mtp) REVERT: A 488 GLU cc_start: 0.8347 (tt0) cc_final: 0.8116 (tt0) REVERT: A 515 LEU cc_start: 0.8938 (tp) cc_final: 0.8712 (tp) outliers start: 10 outliers final: 5 residues processed: 62 average time/residue: 0.7230 time to fit residues: 47.7759 Evaluate side-chains 57 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4547 Z= 0.209 Angle : 0.573 8.185 6202 Z= 0.285 Chirality : 0.041 0.138 690 Planarity : 0.004 0.038 752 Dihedral : 7.110 63.264 600 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.16 % Allowed : 16.45 % Favored : 81.39 % 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: 1.74 (0.37), residues: 544 helix: 1.53 (0.26), residues: 385 sheet: None (None), residues: 0 loop : 0.41 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS A 599 PHE 0.014 0.002 PHE A 409 TYR 0.017 0.001 TYR A 84 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1088 Ramachandran restraints generated. 544 Oldfield, 0 Emsley, 544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.498 Fit side-chains REVERT: A 242 MET cc_start: 0.8598 (mtp) cc_final: 0.8330 (mtp) REVERT: A 336 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (p0) REVERT: A 444 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8417 (tp) REVERT: A 488 GLU cc_start: 0.8444 (tt0) cc_final: 0.8223 (tt0) REVERT: A 515 LEU cc_start: 0.8950 (tp) cc_final: 0.8740 (tp) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.6900 time to fit residues: 44.2416 Evaluate side-chains 60 residues out of total 462 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0293 > 50: distance: 63 - 90: 34.980 distance: 66 - 71: 4.726 distance: 67 - 101: 36.522 distance: 71 - 72: 7.915 distance: 72 - 73: 10.494 distance: 72 - 75: 7.766 distance: 73 - 74: 3.574 distance: 73 - 79: 9.578 distance: 74 - 107: 30.489 distance: 75 - 76: 7.646 distance: 76 - 77: 6.564 distance: 76 - 78: 5.080 distance: 79 - 80: 7.479 distance: 80 - 81: 8.901 distance: 80 - 83: 10.822 distance: 81 - 82: 15.002 distance: 81 - 90: 11.993 distance: 82 - 115: 22.854 distance: 83 - 84: 10.374 distance: 84 - 85: 11.805 distance: 85 - 86: 8.049 distance: 86 - 87: 7.760 distance: 87 - 88: 16.538 distance: 87 - 89: 6.320 distance: 90 - 91: 10.901 distance: 91 - 92: 14.996 distance: 91 - 94: 8.765 distance: 92 - 93: 20.001 distance: 92 - 101: 21.972 distance: 93 - 123: 12.192 distance: 94 - 95: 10.083 distance: 95 - 96: 4.337 distance: 95 - 97: 5.433 distance: 96 - 98: 5.566 distance: 97 - 99: 4.558 distance: 98 - 100: 5.905 distance: 99 - 100: 4.391 distance: 101 - 102: 45.823 distance: 102 - 103: 6.182 distance: 102 - 105: 26.883 distance: 103 - 104: 8.234 distance: 103 - 107: 11.849 distance: 104 - 131: 18.011 distance: 105 - 106: 25.179 distance: 107 - 108: 13.963 distance: 108 - 109: 4.908 distance: 108 - 111: 9.235 distance: 109 - 110: 5.480 distance: 109 - 115: 6.269 distance: 110 - 140: 13.922 distance: 111 - 112: 9.652 distance: 112 - 114: 3.446 distance: 115 - 116: 3.408 distance: 116 - 119: 3.768 distance: 118 - 149: 11.308 distance: 119 - 120: 4.620 distance: 120 - 121: 3.730 distance: 120 - 122: 3.536 distance: 124 - 125: 5.096 distance: 124 - 127: 5.658 distance: 125 - 131: 3.690 distance: 126 - 157: 5.794 distance: 127 - 128: 4.177 distance: 127 - 129: 4.247 distance: 128 - 130: 7.471 distance: 131 - 132: 4.529 distance: 132 - 133: 6.259 distance: 132 - 135: 5.916 distance: 133 - 134: 5.011 distance: 133 - 140: 4.845 distance: 134 - 165: 4.498 distance: 135 - 136: 8.799 distance: 136 - 137: 15.387 distance: 137 - 138: 8.624 distance: 137 - 139: 12.478 distance: 140 - 141: 6.792 distance: 141 - 144: 4.528 distance: 142 - 143: 18.607 distance: 142 - 149: 8.531 distance: 144 - 145: 5.039 distance: 145 - 146: 16.899 distance: 146 - 147: 15.841 distance: 146 - 148: 12.220 distance: 149 - 150: 4.488 distance: 150 - 151: 3.157 distance: 150 - 153: 4.472 distance: 151 - 152: 3.097 distance: 151 - 157: 9.432 distance: 153 - 154: 3.353 distance: 154 - 155: 16.041 distance: 155 - 156: 8.840