Starting phenix.real_space_refine on Mon Jun 24 20:16:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ydq_33756/06_2024/7ydq_33756_updated.pdb" } resolution = 4.04 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3144 2.51 5 N 760 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4778 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4778 Unusual residues: {'IRX': 1} Classifications: {'peptide': 598, 'undetermined': 1} Link IDs: {'PTRANS': 21, 'TRANS': 576, None: 1} Not linked: pdbres="PRO A 652 " pdbres="IRX A 701 " Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 3.20, per 1000 atoms: 0.67 Number of scatterers: 4778 At special positions: 0 Unit cell: (84.7, 68.2, 119.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 846 8.00 N 760 7.00 C 3144 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: 1.69 Conformation dependent library (CDL) restraints added in 821.0 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 47.5% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 32 through 57 removed outlier: 4.648A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 82 removed outlier: 3.661A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.575A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 144 removed outlier: 4.119A pdb=" N THR A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.798A pdb=" N GLY A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.117A pdb=" N LEU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 273 through 291 removed outlier: 4.191A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ARG A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 331 removed outlier: 4.445A pdb=" N SER A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.710A pdb=" N ILE A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.971A pdb=" N THR A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 454 through 460 Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 614 through 643 removed outlier: 4.202A pdb=" N ILE A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 638 " --> pdb=" O CYS A 634 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 640 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 642 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 395 through 405 removed outlier: 6.635A pdb=" N LEU A 489 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLU A 387 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN A 491 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP A 389 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE A 493 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ASP A 391 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 495 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS A 536 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN A 519 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG A 538 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER A 517 " --> pdb=" O ARG A 538 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 708 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: 1.23 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1461 1.34 - 1.46: 1205 1.46 - 1.58: 2184 1.58 - 1.70: 4 1.70 - 1.82: 43 Bond restraints: 4897 Sorted by residual: bond pdb=" C15 IRX A 701 " pdb=" C16 IRX A 701 " ideal model delta sigma weight residual 1.482 1.633 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 IRX A 701 " pdb=" C8 IRX A 701 " ideal model delta sigma weight residual 1.527 1.670 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C18 IRX A 701 " pdb=" C19 IRX A 701 " ideal model delta sigma weight residual 1.455 1.596 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C7 IRX A 701 " pdb=" C8 IRX A 701 " ideal model delta sigma weight residual 1.524 1.642 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C11 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 1.516 1.444 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 4892 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.15: 131 107.15 - 114.43: 2870 114.43 - 121.71: 2630 121.71 - 128.99: 964 128.99 - 136.27: 41 Bond angle restraints: 6636 Sorted by residual: angle pdb=" C12 IRX A 701 " pdb=" N4 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 119.44 136.27 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C10 IRX A 701 " pdb=" C11 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 114.59 99.86 14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 105.48 6.52 1.40e+00 5.10e-01 2.17e+01 angle pdb=" C16 IRX A 701 " pdb=" C15 IRX A 701 " pdb=" N5 IRX A 701 " ideal model delta sigma weight residual 115.43 128.43 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C7 IRX A 701 " pdb=" C9 IRX A 701 " pdb=" N4 IRX A 701 " ideal model delta sigma weight residual 113.70 101.29 12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 6631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2374 16.91 - 33.82: 358 33.82 - 50.73: 104 50.73 - 67.63: 17 67.63 - 84.54: 4 Dihedral angle restraints: 2857 sinusoidal: 1130 harmonic: 1727 Sorted by residual: dihedral pdb=" CA HIS A 587 " pdb=" C HIS A 587 " pdb=" N MET A 588 " pdb=" CA MET A 588 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE A 484 " pdb=" C PHE A 484 " pdb=" N GLU A 485 " pdb=" CA GLU A 485 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS A 334 " pdb=" C HIS A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 433 0.029 - 0.058: 220 0.058 - 0.087: 54 0.087 - 0.116: 40 0.116 - 0.145: 10 Chirality restraints: 757 Sorted by residual: chirality pdb=" CA VAL A 589 " pdb=" N VAL A 589 " pdb=" C VAL A 589 " pdb=" CB VAL A 589 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA PHE A 257 " pdb=" N PHE A 257 " pdb=" C PHE A 257 " pdb=" CB PHE A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A 417 " pdb=" N ILE A 417 " pdb=" C ILE A 417 " pdb=" CB ILE A 417 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 754 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO A 258 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 649 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO A 650 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 650 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 650 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 292 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 293 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.026 5.00e-02 4.00e+02 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1136 2.79 - 3.32: 4589 3.32 - 3.84: 7791 3.84 - 4.37: 8569 4.37 - 4.90: 14560 Nonbonded interactions: 36645 Sorted by model distance: nonbonded pdb=" OG SER A 98 " pdb=" OE1 GLU A 196 " model vdw 2.262 2.440 nonbonded pdb=" O SER A 239 " pdb=" OG SER A 239 " model vdw 2.333 2.440 nonbonded pdb=" N GLN A 115 " pdb=" OE1 GLN A 115 " model vdw 2.340 2.520 nonbonded pdb=" OD1 ASN A 54 " pdb=" OG SER A 160 " model vdw 2.348 2.440 nonbonded pdb=" OD2 ASP A 391 " pdb=" NZ LYS A 396 " model vdw 2.349 2.520 ... (remaining 36640 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 group one per residue 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: 0.350 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: 1.700 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.860 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 4897 Z= 0.296 Angle : 0.828 16.833 6636 Z= 0.386 Chirality : 0.043 0.145 757 Planarity : 0.006 0.119 825 Dihedral : 17.500 84.544 1745 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.57 % Allowed : 27.41 % Favored : 72.02 % 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: 1.21 (0.37), residues: 590 helix: 1.12 (0.35), residues: 250 sheet: 1.69 (0.46), residues: 119 loop : 0.04 (0.47), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 427 HIS 0.009 0.001 HIS A 587 PHE 0.020 0.002 PHE A 484 TYR 0.010 0.001 TYR A 462 ARG 0.003 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.543 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ARG cc_start: 0.6188 (ttt-90) cc_final: 0.5610 (ttp-170) REVERT: A 462 TYR cc_start: 0.8126 (p90) cc_final: 0.7718 (p90) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.1872 time to fit residues: 14.4401 Evaluate side-chains 61 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4897 Z= 0.198 Angle : 0.629 6.191 6636 Z= 0.318 Chirality : 0.044 0.145 757 Planarity : 0.005 0.073 825 Dihedral : 4.692 28.492 639 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.57 % Allowed : 4.73 % Favored : 94.71 % 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: 0.85 (0.36), residues: 590 helix: 0.66 (0.33), residues: 277 sheet: 1.81 (0.46), residues: 122 loop : -0.27 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.007 0.001 HIS A 587 PHE 0.021 0.002 PHE A 139 TYR 0.018 0.001 TYR A 181 ARG 0.001 0.000 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.537 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.5650 (ptpp) cc_final: 0.5310 (ttmt) REVERT: A 340 ILE cc_start: 0.7960 (mm) cc_final: 0.7537 (mm) REVERT: A 443 ARG cc_start: 0.6253 (ttt-90) cc_final: 0.5654 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1870 time to fit residues: 18.5162 Evaluate side-chains 58 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 30.0000 chunk 40 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4897 Z= 0.215 Angle : 0.622 7.312 6636 Z= 0.317 Chirality : 0.044 0.160 757 Planarity : 0.004 0.059 825 Dihedral : 4.438 22.381 639 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.19 % Allowed : 4.35 % Favored : 95.46 % 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: 0.94 (0.37), residues: 590 helix: 0.53 (0.32), residues: 277 sheet: 2.05 (0.47), residues: 121 loop : -0.01 (0.50), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS A 587 PHE 0.017 0.002 PHE A 535 TYR 0.012 0.001 TYR A 181 ARG 0.002 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.538 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.5804 (ptpp) cc_final: 0.5563 (ttmt) REVERT: A 443 ARG cc_start: 0.6356 (ttt-90) cc_final: 0.5732 (ttp-170) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1804 time to fit residues: 17.0950 Evaluate side-chains 56 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.0970 chunk 36 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4897 Z= 0.140 Angle : 0.569 7.603 6636 Z= 0.280 Chirality : 0.041 0.135 757 Planarity : 0.004 0.052 825 Dihedral : 4.112 18.172 639 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.19 % Allowed : 2.08 % Favored : 97.73 % 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: 1.20 (0.37), residues: 590 helix: 0.92 (0.33), residues: 270 sheet: 1.96 (0.46), residues: 122 loop : 0.00 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.005 0.001 HIS A 551 PHE 0.010 0.001 PHE A 288 TYR 0.010 0.001 TYR A 444 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.505 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.5740 (ptpp) cc_final: 0.5520 (ttmt) REVERT: A 385 LEU cc_start: 0.8697 (mm) cc_final: 0.8141 (tt) outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1790 time to fit residues: 17.4316 Evaluate side-chains 57 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.0741 > 50: distance: 26 - 132: 31.239 distance: 29 - 129: 15.518 distance: 40 - 115: 28.631 distance: 43 - 112: 29.930 distance: 76 - 124: 24.180 distance: 79 - 121: 13.378 distance: 86 - 106: 35.870 distance: 89 - 103: 23.343 distance: 99 - 103: 24.874 distance: 103 - 104: 8.601 distance: 104 - 105: 13.474 distance: 104 - 107: 13.322 distance: 105 - 106: 14.158 distance: 105 - 112: 28.494 distance: 107 - 108: 8.616 distance: 108 - 109: 19.193 distance: 109 - 110: 8.704 distance: 109 - 111: 4.304 distance: 112 - 113: 9.603 distance: 113 - 114: 14.653 distance: 113 - 116: 13.599 distance: 114 - 115: 9.199 distance: 114 - 121: 25.732 distance: 116 - 117: 25.955 distance: 117 - 118: 21.404 distance: 118 - 119: 18.017 distance: 118 - 120: 20.691 distance: 121 - 122: 17.774 distance: 122 - 123: 26.799 distance: 122 - 125: 13.799 distance: 123 - 124: 18.950 distance: 123 - 129: 23.295 distance: 125 - 126: 23.884 distance: 126 - 127: 46.170 distance: 126 - 128: 28.327 distance: 129 - 130: 17.258 distance: 130 - 131: 37.287 distance: 130 - 133: 14.302 distance: 131 - 132: 15.017 distance: 131 - 136: 14.041 distance: 133 - 134: 42.034 distance: 133 - 135: 8.229 distance: 136 - 137: 14.618 distance: 136 - 142: 29.876 distance: 137 - 138: 13.740 distance: 138 - 139: 11.541 distance: 138 - 143: 7.410 distance: 140 - 141: 40.036 distance: 141 - 142: 19.614 distance: 143 - 144: 25.542 distance: 144 - 145: 24.755 distance: 144 - 147: 22.287 distance: 145 - 146: 33.263 distance: 145 - 151: 12.677 distance: 147 - 148: 17.769 distance: 147 - 149: 25.404 distance: 148 - 150: 7.499 distance: 151 - 152: 42.702 distance: 152 - 153: 21.433 distance: 153 - 154: 43.098 distance: 153 - 155: 29.560 distance: 155 - 156: 14.980 distance: 156 - 157: 21.828 distance: 156 - 159: 28.675 distance: 157 - 158: 10.910 distance: 157 - 163: 29.859 distance: 159 - 160: 36.080 distance: 160 - 161: 19.458 distance: 160 - 162: 7.953 distance: 163 - 164: 11.450 distance: 164 - 165: 17.211 distance: 165 - 166: 6.860 distance: 165 - 167: 11.134 distance: 167 - 168: 8.129 distance: 167 - 173: 29.705 distance: 168 - 169: 5.331 distance: 168 - 171: 9.832 distance: 169 - 170: 21.913 distance: 169 - 174: 21.477 distance: 171 - 172: 30.194 distance: 172 - 173: 12.688