Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 06:32:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/10_2023/7t4k_25678_updated.pdb" } resolution = 3.25 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= 0.009 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 2 5.49 5 S 41 5.16 5 C 3941 2.51 5 N 1048 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 6180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3039 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3141 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 3.64, per 1000 atoms: 0.59 Number of scatterers: 6180 At special positions: 0 Unit cell: (115.44, 78, 73.32, 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 41 16.00 P 2 15.00 O 1148 8.00 N 1048 7.00 C 3941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 7 sheets defined 38.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.435A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 389 through 392 No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.564A pdb=" N ALA A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.531A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.737A pdb=" N GLY B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 134 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 137 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.895A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 558 through 573 Processing sheet with id= A, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.721A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 340 through 343 Processing sheet with id= C, first strand: chain 'A' and resid 370 through 372 Processing sheet with id= D, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.558A pdb=" N LYS B 177 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 286 " --> pdb=" O MET B 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= F, first strand: chain 'B' and resid 370 through 372 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 167 removed outlier: 7.052A pdb=" N VAL B 173 " --> pdb=" O ILE B 165 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 618 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: 1.47 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1988 1.34 - 1.46: 1125 1.46 - 1.58: 3112 1.58 - 1.69: 8 1.69 - 1.81: 65 Bond restraints: 6298 Sorted by residual: bond pdb=" C VAL B 216 " pdb=" N PRO B 217 " ideal model delta sigma weight residual 1.334 1.374 -0.041 2.34e-02 1.83e+03 3.00e+00 bond pdb=" C LEU A 543 " pdb=" N PRO A 544 " ideal model delta sigma weight residual 1.334 1.359 -0.024 1.51e-02 4.39e+03 2.60e+00 bond pdb=" CB ASP B 442 " pdb=" CG ASP B 442 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.50e+00 bond pdb=" CG LEU A 571 " pdb=" CD1 LEU A 571 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" C LEU B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.35e+00 ... (remaining 6293 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.10: 137 105.10 - 112.35: 3168 112.35 - 119.60: 2152 119.60 - 126.85: 2986 126.85 - 134.10: 89 Bond angle restraints: 8532 Sorted by residual: angle pdb=" CA GLU A 214 " pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA MET B 249 " pdb=" CB MET B 249 " pdb=" CG MET B 249 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" N GLU B 441 " pdb=" CA GLU B 441 " pdb=" C GLU B 441 " ideal model delta sigma weight residual 111.36 115.39 -4.03 1.09e+00 8.42e-01 1.37e+01 angle pdb=" CB MET B 195 " pdb=" CG MET B 195 " pdb=" SD MET B 195 " ideal model delta sigma weight residual 112.70 101.71 10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " pdb=" CD GLN A 569 " ideal model delta sigma weight residual 112.60 118.81 -6.21 1.70e+00 3.46e-01 1.33e+01 ... (remaining 8527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3498 16.79 - 33.58: 296 33.58 - 50.37: 46 50.37 - 67.16: 7 67.16 - 83.95: 6 Dihedral angle restraints: 3853 sinusoidal: 1537 harmonic: 2316 Sorted by residual: dihedral pdb=" CA SER B 280 " pdb=" C SER B 280 " pdb=" N GLY B 281 " pdb=" CA GLY B 281 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN A 326 " pdb=" CB ASN A 326 " pdb=" CG ASN A 326 " pdb=" OD1 ASN A 326 " ideal model delta sinusoidal sigma weight residual 120.00 -173.25 -66.75 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP B 121 " pdb=" CB ASP B 121 " pdb=" CG ASP B 121 " pdb=" OD1 ASP B 121 " ideal model delta sinusoidal sigma weight residual -30.00 -84.01 54.01 1 2.00e+01 2.50e-03 9.90e+00 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 693 0.048 - 0.095: 201 0.095 - 0.143: 61 0.143 - 0.191: 14 0.191 - 0.239: 2 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA GLU A 158 " pdb=" N GLU A 158 " pdb=" C GLU A 158 " pdb=" CB GLU A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 968 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 439 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LYS B 439 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 440 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 125 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C GLU B 125 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 125 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 126 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 129 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TRP B 129 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP B 129 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 130 " 0.011 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1574 2.81 - 3.33: 5766 3.33 - 3.85: 9649 3.85 - 4.38: 11796 4.38 - 4.90: 20271 Nonbonded interactions: 49056 Sorted by model distance: nonbonded pdb=" OE2 GLU B 346 " pdb=" OG1 THR B 352 " model vdw 2.287 2.440 nonbonded pdb=" ND2 ASN B 197 " pdb=" O MET B 284 " model vdw 2.361 2.520 nonbonded pdb=" OE2 GLU A 320 " pdb=" NH2 ARG A 555 " model vdw 2.379 2.520 nonbonded pdb=" OE2 GLU B 320 " pdb=" NH2 ARG B 555 " model vdw 2.388 2.520 nonbonded pdb=" O TYR B 212 " pdb=" NH1 ARG B 239 " model vdw 2.397 2.520 ... (remaining 49051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 200 or (resid 201 and (name N or name CA or name C or n \ ame O or name CB )) or resid 202 through 223 or (resid 237 and (name N or name C \ A or name C or name O or name CB )) or resid 238 through 493 or (resid 494 and ( \ name N or name CA or name C or name O or name CB )) or resid 495 through 574)) selection = (chain 'B' and (resid 120 through 136 or resid 148 through 256 or (resid 282 and \ (name N or name CA or name C or name O or name CB )) or resid 283 through 511 o \ r resid 541 through 574)) } 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: 3.270 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: 16.620 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.110 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.005 0.070 6298 Z= 0.302 Angle : 0.881 11.701 8532 Z= 0.468 Chirality : 0.051 0.239 971 Planarity : 0.006 0.046 1080 Dihedral : 12.764 83.950 2339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % 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: 0.51 (0.30), residues: 754 helix: 1.27 (0.28), residues: 298 sheet: -0.64 (0.49), residues: 114 loop : -0.02 (0.33), residues: 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.745 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1626 time to fit residues: 22.3889 Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 366 GLN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6298 Z= 0.229 Angle : 0.496 6.243 8532 Z= 0.253 Chirality : 0.039 0.145 971 Planarity : 0.004 0.035 1080 Dihedral : 5.798 78.319 847 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.50 % Allowed : 5.55 % Favored : 92.95 % 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: 1.27 (0.30), residues: 754 helix: 2.09 (0.28), residues: 304 sheet: -0.42 (0.47), residues: 114 loop : 0.24 (0.34), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.740 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.1623 time to fit residues: 20.1660 Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0603 time to fit residues: 1.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 366 GLN B 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6298 Z= 0.270 Angle : 0.491 5.935 8532 Z= 0.250 Chirality : 0.040 0.140 971 Planarity : 0.004 0.038 1080 Dihedral : 5.793 76.016 847 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.60 % Allowed : 8.55 % Favored : 90.85 % 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: 1.45 (0.31), residues: 754 helix: 2.24 (0.29), residues: 306 sheet: -0.31 (0.47), residues: 114 loop : 0.33 (0.35), residues: 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.742 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 80 average time/residue: 0.1618 time to fit residues: 18.2500 Evaluate side-chains 75 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 70 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN B 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6298 Z= 0.152 Angle : 0.438 5.254 8532 Z= 0.224 Chirality : 0.038 0.138 971 Planarity : 0.004 0.034 1080 Dihedral : 5.714 74.978 847 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.20 % Allowed : 8.85 % Favored : 89.96 % 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: 1.69 (0.31), residues: 754 helix: 2.42 (0.29), residues: 307 sheet: -0.19 (0.47), residues: 114 loop : 0.49 (0.35), residues: 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.677 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.1724 time to fit residues: 20.2153 Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0624 time to fit residues: 1.3773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6298 Z= 0.242 Angle : 0.476 6.884 8532 Z= 0.240 Chirality : 0.039 0.138 971 Planarity : 0.004 0.035 1080 Dihedral : 5.701 75.019 847 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.05 % Allowed : 10.34 % Favored : 88.61 % 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: 1.61 (0.31), residues: 754 helix: 2.38 (0.29), residues: 307 sheet: -0.32 (0.46), residues: 114 loop : 0.44 (0.35), residues: 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.742 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 83 average time/residue: 0.1719 time to fit residues: 19.7074 Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.740 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0682 time to fit residues: 1.1767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 60.1788 > 50: distance: 7 - 9: 6.805 distance: 10 - 11: 5.816 distance: 11 - 12: 4.838 distance: 14 - 15: 30.537 distance: 15 - 16: 41.726 distance: 15 - 18: 29.245 distance: 16 - 17: 21.502 distance: 16 - 21: 35.727 distance: 18 - 19: 19.859 distance: 18 - 20: 34.089 distance: 21 - 22: 18.373 distance: 22 - 23: 16.972 distance: 22 - 25: 43.696 distance: 23 - 24: 34.757 distance: 23 - 30: 27.298 distance: 25 - 26: 36.228 distance: 26 - 27: 19.864 distance: 27 - 28: 10.069 distance: 27 - 29: 31.394 distance: 30 - 31: 6.968 distance: 31 - 32: 41.323 distance: 31 - 34: 36.353 distance: 32 - 33: 37.686 distance: 32 - 39: 36.764 distance: 34 - 35: 33.957 distance: 35 - 36: 33.060 distance: 36 - 37: 26.356 distance: 36 - 38: 36.161 distance: 39 - 40: 18.368 distance: 40 - 41: 18.833 distance: 40 - 43: 21.066 distance: 41 - 42: 12.958 distance: 41 - 47: 25.114 distance: 43 - 44: 25.214 distance: 44 - 45: 11.640 distance: 44 - 46: 41.772 distance: 47 - 48: 30.580 distance: 48 - 49: 13.847 distance: 48 - 51: 15.358 distance: 49 - 50: 14.689 distance: 49 - 56: 40.053 distance: 51 - 52: 41.462 distance: 52 - 53: 18.547 distance: 53 - 54: 18.984 distance: 53 - 55: 28.686 distance: 56 - 57: 35.938 distance: 57 - 58: 29.342 distance: 57 - 60: 18.062 distance: 58 - 59: 40.062 distance: 58 - 61: 41.712 distance: 61 - 62: 24.246 distance: 62 - 63: 13.485 distance: 62 - 65: 22.694 distance: 63 - 64: 17.527 distance: 63 - 66: 34.903 distance: 66 - 67: 9.873 distance: 67 - 68: 13.052 distance: 67 - 70: 29.644 distance: 68 - 69: 28.167 distance: 68 - 74: 48.944 distance: 70 - 71: 28.712 distance: 71 - 72: 42.277 distance: 71 - 73: 24.743 distance: 74 - 75: 7.489 distance: 75 - 76: 19.565 distance: 75 - 78: 21.303 distance: 76 - 77: 30.002 distance: 76 - 82: 28.272 distance: 78 - 79: 21.297 distance: 79 - 80: 28.204 distance: 79 - 81: 46.092