Starting phenix.real_space_refine on Wed Jan 17 18:18:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1q_35930/01_2024/8j1q_35930_updated.pdb" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 90 5.49 5 S 15 5.16 5 C 3213 2.51 5 N 918 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 428": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5447 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 1008 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Chain: "D" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1138 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Chain: "A" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 942 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "C" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1562 Unusual residues: {'NAG': 1} Classifications: {'peptide': 196, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184, None: 1} Not linked: pdbres="LYS C 528 " pdbres="NAG C 701 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.67 Number of scatterers: 5447 At special positions: 0 Unit cell: (66.42, 104.14, 115.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 90 15.00 O 1211 8.00 N 918 7.00 C 3213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 Links applied NAG-ASN " NAG C 701 " - " ASN C 343 " Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 644.5 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 7 sheets defined 9.6% alpha, 24.8% beta 3 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 384 through 389 removed outlier: 5.059A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.193A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 11 removed outlier: 5.655A pdb=" N LYS A 106 " --> pdb=" O VAL A 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 17 through 23 Processing sheet with id= C, first strand: chain 'A' and resid 87 through 91 removed outlier: 5.734A pdb=" N GLN A 39 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LEU A 48 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= E, first strand: chain 'B' and resid 114 through 116 removed outlier: 5.802A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.520A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 452 through 454 77 hydrogen bonds defined for protein. 189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 2.94 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: 669 1.30 - 1.43: 2223 1.43 - 1.56: 2639 1.56 - 1.70: 229 1.70 - 1.83: 40 Bond restraints: 5800 Sorted by residual: bond pdb=" C2' 85Y D 24 " pdb=" C1' 85Y D 24 " ideal model delta sigma weight residual 1.280 1.571 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C2' 85Y D 43 " pdb=" C1' 85Y D 43 " ideal model delta sigma weight residual 1.280 1.570 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C2' 85Y E 55 " pdb=" C1' 85Y E 55 " ideal model delta sigma weight residual 1.280 1.569 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C2' 85Y D 34 " pdb=" C1' 85Y D 34 " ideal model delta sigma weight residual 1.280 1.565 -0.285 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C2' 85Y E 59 " pdb=" C1' 85Y E 59 " ideal model delta sigma weight residual 1.280 1.564 -0.284 2.00e-02 2.50e+03 2.02e+02 ... (remaining 5795 not shown) Histogram of bond angle deviations from ideal: 90.27 - 102.23: 61 102.23 - 114.19: 3671 114.19 - 126.14: 4213 126.14 - 138.10: 316 138.10 - 150.06: 22 Bond angle restraints: 8283 Sorted by residual: angle pdb=" C23 85Y D 30 " pdb=" C24 85Y D 30 " pdb=" C25 85Y D 30 " ideal model delta sigma weight residual 125.08 150.06 -24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" C23 85Y D 34 " pdb=" C24 85Y D 34 " pdb=" C25 85Y D 34 " ideal model delta sigma weight residual 125.08 150.01 -24.93 3.00e+00 1.11e-01 6.90e+01 angle pdb=" C23 85Y E 48 " pdb=" C24 85Y E 48 " pdb=" C25 85Y E 48 " ideal model delta sigma weight residual 125.08 149.59 -24.51 3.00e+00 1.11e-01 6.67e+01 angle pdb=" C23 85Y E 59 " pdb=" C24 85Y E 59 " pdb=" C25 85Y E 59 " ideal model delta sigma weight residual 125.08 149.08 -24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C23 85Y D 43 " pdb=" C24 85Y D 43 " pdb=" C25 85Y D 43 " ideal model delta sigma weight residual 125.08 148.94 -23.86 3.00e+00 1.11e-01 6.32e+01 ... (remaining 8278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 2596 35.55 - 71.09: 388 71.09 - 106.64: 27 106.64 - 142.18: 3 142.18 - 177.72: 11 Dihedral angle restraints: 3025 sinusoidal: 1799 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 18.15 74.85 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 45.27 47.73 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" CA CYS C 391 " pdb=" C CYS C 391 " pdb=" N PHE C 392 " pdb=" CA PHE C 392 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 3022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 606 0.046 - 0.093: 164 0.093 - 0.139: 44 0.139 - 0.185: 19 0.185 - 0.232: 2 Chirality restraints: 835 Sorted by residual: chirality pdb=" C3' 85Y E 59 " pdb=" C4' 85Y E 59 " pdb=" O3' 85Y E 59 " pdb=" C2' 85Y E 59 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' 85Y D 17 " pdb=" C4' 85Y D 17 " pdb=" O3' 85Y D 17 " pdb=" C2' 85Y D 17 " both_signs ideal model delta sigma weight residual False -2.57 -2.35 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1' 85Y D 35 " pdb=" O4' 85Y D 35 " pdb=" C2' 85Y D 35 " pdb=" N1 85Y D 35 " both_signs ideal model delta sigma weight residual False 2.40 2.59 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 832 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.018 2.00e-02 2.50e+03 2.01e-02 5.03e+00 pdb=" CG ASN C 343 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 48 " 0.018 2.00e-02 2.50e+03 8.50e-03 2.17e+00 pdb=" N9 DG D 48 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DG D 48 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG D 48 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 48 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG D 48 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG D 48 " 0.009 2.00e-02 2.50e+03 pdb=" N2 DG D 48 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DG D 48 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG D 48 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 25 " -0.014 2.00e-02 2.50e+03 6.32e-03 1.20e+00 pdb=" N9 DG E 25 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DG E 25 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DG E 25 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG E 25 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG E 25 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG E 25 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG E 25 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 25 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG E 25 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG E 25 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG E 25 " 0.001 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 146 2.61 - 3.19: 4827 3.19 - 3.76: 8699 3.76 - 4.33: 11650 4.33 - 4.90: 18454 Nonbonded interactions: 43776 Sorted by model distance: nonbonded pdb=" OH TYR B 35 " pdb=" O ASP B 104 " model vdw 2.043 2.440 nonbonded pdb=" N6 DA E 35 " pdb=" O SER C 494 " model vdw 2.074 2.520 nonbonded pdb=" OP2 85Y D 43 " pdb=" O3' 85Y D 43 " model vdw 2.119 2.440 nonbonded pdb=" O2 DC E 36 " pdb=" OH TYR C 505 " model vdw 2.145 2.440 nonbonded pdb=" O ASP A 84 " pdb=" OH TYR A 88 " model vdw 2.208 2.440 ... (remaining 43771 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=0.00 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: 0.760 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: 3.630 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.120 Find NCS groups from input model: 0.140 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 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 : 0.030 0.291 5800 Z= 1.478 Angle : 1.931 24.981 8283 Z= 0.687 Chirality : 0.051 0.232 835 Planarity : 0.002 0.019 727 Dihedral : 28.591 177.724 2237 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.28 % Allowed : 22.35 % Favored : 77.37 % 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: -1.02 (0.41), residues: 421 helix: -3.43 (0.72), residues: 32 sheet: -0.28 (0.47), residues: 128 loop : -0.45 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 37 HIS 0.001 0.000 HIS C 519 PHE 0.011 0.001 PHE C 392 TYR 0.009 0.001 TYR B 35 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.461 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.2083 time to fit residues: 17.9783 Evaluate side-chains 60 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5800 Z= 0.270 Angle : 1.364 14.194 8283 Z= 0.521 Chirality : 0.044 0.208 835 Planarity : 0.003 0.018 727 Dihedral : 31.417 178.098 1531 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.35 % Allowed : 23.74 % Favored : 72.91 % 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: -0.79 (0.42), residues: 421 helix: -3.07 (0.79), residues: 32 sheet: -0.02 (0.47), residues: 130 loop : -0.38 (0.40), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 37 HIS 0.001 0.001 HIS A 41 PHE 0.013 0.002 PHE B 29 TYR 0.013 0.001 TYR B 35 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.508 Fit side-chains REVERT: B 79 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7709 (tp) outliers start: 12 outliers final: 7 residues processed: 70 average time/residue: 0.1904 time to fit residues: 17.1569 Evaluate side-chains 63 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 54.1327 > 50: distance: 8 - 113: 16.582 distance: 11 - 110: 18.490 distance: 53 - 54: 3.605 distance: 53 - 59: 4.193 distance: 54 - 55: 8.043 distance: 54 - 57: 3.742 distance: 55 - 56: 5.514 distance: 55 - 60: 11.942 distance: 58 - 59: 3.301 distance: 60 - 61: 9.930 distance: 61 - 62: 6.019 distance: 62 - 63: 10.448 distance: 62 - 64: 8.586 distance: 64 - 65: 8.382 distance: 65 - 66: 4.415 distance: 65 - 68: 8.491 distance: 66 - 67: 5.561 distance: 66 - 73: 8.254 distance: 68 - 69: 10.796 distance: 69 - 70: 10.295 distance: 70 - 71: 13.624 distance: 71 - 72: 11.875 distance: 74 - 75: 7.751 distance: 74 - 77: 14.285 distance: 75 - 76: 18.307 distance: 75 - 78: 5.610 distance: 78 - 79: 8.236 distance: 78 - 84: 17.686 distance: 79 - 80: 3.417 distance: 79 - 82: 3.355 distance: 80 - 81: 9.464 distance: 80 - 85: 7.680 distance: 82 - 83: 14.401 distance: 83 - 84: 4.870 distance: 85 - 86: 8.497 distance: 86 - 87: 7.185 distance: 86 - 89: 7.460 distance: 87 - 88: 18.570 distance: 89 - 90: 16.035 distance: 90 - 91: 8.703 distance: 91 - 92: 13.968 distance: 92 - 93: 9.399 distance: 94 - 95: 11.615 distance: 95 - 96: 4.228 distance: 95 - 98: 9.210 distance: 96 - 97: 31.563 distance: 96 - 102: 21.468 distance: 98 - 99: 8.035 distance: 99 - 100: 9.408 distance: 99 - 101: 5.480 distance: 102 - 103: 9.296 distance: 103 - 104: 24.008 distance: 103 - 106: 19.821 distance: 104 - 105: 17.854 distance: 104 - 110: 18.923 distance: 106 - 107: 10.484 distance: 107 - 108: 11.261 distance: 108 - 109: 17.899 distance: 110 - 111: 7.107 distance: 111 - 112: 17.356 distance: 111 - 114: 7.950 distance: 112 - 113: 6.041 distance: 112 - 118: 4.740 distance: 114 - 115: 5.502 distance: 114 - 116: 13.121 distance: 115 - 117: 32.285 distance: 118 - 119: 5.339 distance: 119 - 120: 9.216 distance: 119 - 122: 17.701 distance: 120 - 121: 6.645 distance: 120 - 130: 5.473 distance: 122 - 123: 14.977 distance: 123 - 124: 10.183 distance: 123 - 125: 9.254 distance: 124 - 126: 11.122 distance: 125 - 127: 9.395 distance: 126 - 128: 3.513 distance: 127 - 128: 8.908 distance: 128 - 129: 9.339