Starting phenix.real_space_refine on Fri Nov 15 13:10:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/11_2024/8fy3_29551.cif" } resolution = 2.88 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= 0.058 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 55 5.16 5 C 5739 2.51 5 N 1537 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4520 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 25, 'TRANS': 535} Chain breaks: 6 Chain: "B" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4114 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 504} Chain breaks: 6 Chain: "C" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 7, 'TRANS': 30} Time building chain proxies: 6.30, per 1000 atoms: 0.70 Number of scatterers: 8948 At special positions: 0 Unit cell: (69.3, 107.415, 178.101, 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 55 16.00 O 1617 8.00 N 1537 7.00 C 5739 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 - 3.00 Amino acid : True - 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: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 71.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.669A pdb=" N HIS A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 82 removed outlier: 3.760A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.188A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.525A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.705A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.986A pdb=" N LEU A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.517A pdb=" N VAL A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.045A pdb=" N TRP A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.761A pdb=" N ILE A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.925A pdb=" N PHE A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.641A pdb=" N HIS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 496 through 511 Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.789A pdb=" N ILE A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 removed outlier: 3.786A pdb=" N MET A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.615A pdb=" N ILE A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.767A pdb=" N TRP A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 60 through 75 removed outlier: 4.018A pdb=" N ILE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.509A pdb=" N SER B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 331 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.757A pdb=" N GLU B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 403 removed outlier: 3.686A pdb=" N ASN B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.633A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.595A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.670A pdb=" N ALA B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 672 removed outlier: 3.518A pdb=" N LYS B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.551A pdb=" N ILE B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1575 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: 2.57 Time building geometry restraints manager: 2.44 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: 2912 1.34 - 1.46: 1860 1.46 - 1.58: 4286 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 9137 Sorted by residual: bond pdb=" CA PRO B 679 " pdb=" C PRO B 679 " ideal model delta sigma weight residual 1.514 1.520 -0.005 5.50e-03 3.31e+04 9.83e-01 bond pdb=" N TYR B 634 " pdb=" CA TYR B 634 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.80e-01 bond pdb=" C TYR B 634 " pdb=" N PRO B 635 " ideal model delta sigma weight residual 1.340 1.364 -0.023 2.76e-02 1.31e+03 7.25e-01 bond pdb=" CB PRO B 635 " pdb=" CG PRO B 635 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.13e-01 bond pdb=" CG GLU A 261 " pdb=" CD GLU A 261 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.65e-01 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 12238 2.05 - 4.10: 103 4.10 - 6.15: 14 6.15 - 8.19: 1 8.19 - 10.24: 1 Bond angle restraints: 12357 Sorted by residual: angle pdb=" CA TRP C 312 " pdb=" CB TRP C 312 " pdb=" CG TRP C 312 " ideal model delta sigma weight residual 113.60 118.72 -5.12 1.90e+00 2.77e-01 7.27e+00 angle pdb=" C LYS A 23 " pdb=" N ASN A 24 " pdb=" CA ASN A 24 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 angle pdb=" C ILE C 310 " pdb=" N GLN C 311 " pdb=" CA GLN C 311 " ideal model delta sigma weight residual 122.39 119.18 3.21 1.64e+00 3.72e-01 3.83e+00 angle pdb=" CA LEU A 240 " pdb=" CB LEU A 240 " pdb=" CG LEU A 240 " ideal model delta sigma weight residual 116.30 122.89 -6.59 3.50e+00 8.16e-02 3.54e+00 angle pdb=" CA ARG B 84 " pdb=" CB ARG B 84 " pdb=" CG ARG B 84 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.53e+00 ... (remaining 12352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5187 17.23 - 34.45: 272 34.45 - 51.68: 62 51.68 - 68.91: 13 68.91 - 86.13: 3 Dihedral angle restraints: 5537 sinusoidal: 2236 harmonic: 3301 Sorted by residual: dihedral pdb=" CA SER B 241 " pdb=" C SER B 241 " pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN C 311 " pdb=" C GLN C 311 " pdb=" N TRP C 312 " pdb=" CA TRP C 312 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB ARG A 211 " pdb=" CG ARG A 211 " pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " ideal model delta sinusoidal sigma weight residual -180.00 -121.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 797 0.027 - 0.053: 401 0.053 - 0.080: 141 0.080 - 0.107: 50 0.107 - 0.133: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ILE C 310 " pdb=" N ILE C 310 " pdb=" C ILE C 310 " pdb=" CB ILE C 310 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 475 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 476 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 241 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 312 " -0.013 2.00e-02 2.50e+03 8.38e-03 1.75e+00 pdb=" CG TRP C 312 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 312 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 312 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 312 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 312 " -0.001 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 400 2.73 - 3.27: 9333 3.27 - 3.81: 15008 3.81 - 4.36: 17488 4.36 - 4.90: 30067 Nonbonded interactions: 72296 Sorted by model distance: nonbonded pdb=" O ILE A 368 " pdb=" OG SER A 407 " model vdw 2.186 3.040 nonbonded pdb=" O SER B 75 " pdb=" OG1 THR B 78 " model vdw 2.187 3.040 nonbonded pdb=" NE2 GLN A 102 " pdb=" OG SER A 104 " model vdw 2.222 3.120 nonbonded pdb=" O LEU B 158 " pdb=" OG1 THR B 162 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 138 " pdb=" OD1 ASP A 140 " model vdw 2.229 3.040 ... (remaining 72291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.140 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9137 Z= 0.202 Angle : 0.492 10.243 12357 Z= 0.255 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.041 1577 Dihedral : 11.506 86.133 3383 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.96 % Allowed : 6.33 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.07 (0.26), residues: 1093 helix: 1.55 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 312 HIS 0.003 0.001 HIS B 303 PHE 0.012 0.002 PHE B 571 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.029 Fit side-chains REVERT: A 73 PHE cc_start: 0.7729 (t80) cc_final: 0.7143 (t80) REVERT: A 360 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6534 (tm-30) REVERT: A 547 MET cc_start: 0.2744 (mmt) cc_final: 0.2518 (mmt) REVERT: A 617 MET cc_start: 0.4735 (pmm) cc_final: 0.2549 (ttm) REVERT: B 73 PHE cc_start: 0.7544 (m-10) cc_final: 0.7328 (m-10) REVERT: B 135 LYS cc_start: 0.6496 (mtmt) cc_final: 0.5714 (ttpp) REVERT: B 292 ARG cc_start: 0.7206 (mtt90) cc_final: 0.6476 (mtp85) REVERT: B 322 GLU cc_start: 0.7040 (tp30) cc_final: 0.6713 (tp30) REVERT: B 331 SER cc_start: 0.7306 (t) cc_final: 0.7079 (p) REVERT: B 344 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7933 (ttm170) REVERT: B 347 CYS cc_start: 0.8111 (m) cc_final: 0.7678 (p) REVERT: B 370 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7264 (mtt-85) REVERT: B 525 LYS cc_start: 0.7238 (tttp) cc_final: 0.6417 (pmtt) REVERT: B 575 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 29 outliers final: 6 residues processed: 192 average time/residue: 1.1796 time to fit residues: 243.2369 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 410 GLN B 85 GLN B 95 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9137 Z= 0.265 Angle : 0.575 10.921 12357 Z= 0.283 Chirality : 0.039 0.138 1393 Planarity : 0.004 0.065 1577 Dihedral : 5.063 55.480 1207 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.88 % Allowed : 11.24 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.06 (0.26), residues: 1093 helix: 1.46 (0.19), residues: 781 sheet: None (None), residues: 0 loop : -1.22 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 312 HIS 0.005 0.001 HIS C 292 PHE 0.014 0.002 PHE A 206 TYR 0.011 0.001 TYR B 355 ARG 0.011 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.922 Fit side-chains REVERT: A 42 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6936 (tp30) REVERT: A 360 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6502 (tm-30) REVERT: A 362 ASP cc_start: 0.6635 (m-30) cc_final: 0.5663 (p0) REVERT: A 547 MET cc_start: 0.2704 (mmt) cc_final: 0.2496 (mmt) REVERT: A 617 MET cc_start: 0.4628 (pmm) cc_final: 0.4365 (pmm) REVERT: B 135 LYS cc_start: 0.6551 (mtmt) cc_final: 0.5941 (ttpp) REVERT: B 344 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7869 (ttm170) REVERT: B 347 CYS cc_start: 0.8142 (m) cc_final: 0.7779 (p) REVERT: B 525 LYS cc_start: 0.7270 (tttp) cc_final: 0.6372 (pmtt) REVERT: B 558 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7103 (ttpm) REVERT: C 293 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7569 (mp) outliers start: 38 outliers final: 13 residues processed: 134 average time/residue: 0.9595 time to fit residues: 140.6111 Evaluate side-chains 112 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 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 70 GLN A 125 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9137 Z= 0.184 Angle : 0.517 10.469 12357 Z= 0.253 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.056 1577 Dihedral : 4.599 55.073 1203 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.68 % Allowed : 12.67 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.24 (0.26), residues: 1093 helix: 1.61 (0.19), residues: 779 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 312 HIS 0.003 0.001 HIS C 292 PHE 0.012 0.001 PHE A 196 TYR 0.010 0.001 TYR B 355 ARG 0.004 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6912 (tp30) REVERT: A 73 PHE cc_start: 0.7880 (t80) cc_final: 0.7564 (t80) REVERT: A 360 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6500 (tm-30) REVERT: A 362 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.5622 (p0) REVERT: A 617 MET cc_start: 0.4609 (pmm) cc_final: 0.2467 (ttm) REVERT: B 135 LYS cc_start: 0.6535 (mtmt) cc_final: 0.5879 (ttpp) REVERT: B 344 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7805 (ttm170) REVERT: B 347 CYS cc_start: 0.8146 (m) cc_final: 0.7782 (p) REVERT: B 525 LYS cc_start: 0.7270 (tttp) cc_final: 0.6386 (pmtt) REVERT: B 558 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7211 (ttpt) REVERT: C 293 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7523 (mp) outliers start: 36 outliers final: 12 residues processed: 126 average time/residue: 1.0365 time to fit residues: 141.7514 Evaluate side-chains 110 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 405 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9137 Z= 0.224 Angle : 0.529 10.653 12357 Z= 0.260 Chirality : 0.037 0.133 1393 Planarity : 0.004 0.059 1577 Dihedral : 4.616 55.793 1203 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.17 % Allowed : 13.69 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.35 (0.26), residues: 1093 helix: 1.69 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -1.06 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.014 0.002 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.004 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 1.030 Fit side-chains REVERT: A 42 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: A 73 PHE cc_start: 0.7902 (t80) cc_final: 0.7595 (t80) REVERT: A 77 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 360 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6509 (tm-30) REVERT: A 362 ASP cc_start: 0.6753 (m-30) cc_final: 0.5644 (p0) REVERT: A 459 ARG cc_start: 0.7053 (tpm170) cc_final: 0.5384 (ttm110) REVERT: A 617 MET cc_start: 0.4595 (pmm) cc_final: 0.2425 (ttm) REVERT: B 135 LYS cc_start: 0.6603 (mtmt) cc_final: 0.5945 (ttpp) REVERT: B 347 CYS cc_start: 0.8121 (m) cc_final: 0.7771 (p) REVERT: B 525 LYS cc_start: 0.7283 (tttp) cc_final: 0.6339 (pmtt) REVERT: B 558 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7202 (ttpt) REVERT: B 575 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7535 (mp) REVERT: C 293 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7535 (mp) outliers start: 31 outliers final: 14 residues processed: 124 average time/residue: 1.0089 time to fit residues: 136.1954 Evaluate side-chains 115 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9137 Z= 0.305 Angle : 0.573 10.844 12357 Z= 0.281 Chirality : 0.039 0.136 1393 Planarity : 0.004 0.065 1577 Dihedral : 4.418 59.156 1201 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.88 % Allowed : 13.89 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.16 (0.26), residues: 1093 helix: 1.49 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 312 HIS 0.006 0.001 HIS B 303 PHE 0.016 0.002 PHE A 196 TYR 0.013 0.001 TYR B 355 ARG 0.004 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.997 Fit side-chains REVERT: A 33 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7653 (tp-100) REVERT: A 37 ASN cc_start: 0.7345 (p0) cc_final: 0.7015 (p0) REVERT: A 73 PHE cc_start: 0.7930 (t80) cc_final: 0.7664 (t80) REVERT: A 77 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 360 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6510 (tm-30) REVERT: A 362 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6563 (t0) REVERT: A 617 MET cc_start: 0.4557 (pmm) cc_final: 0.2384 (ttm) REVERT: B 63 ILE cc_start: 0.8319 (mm) cc_final: 0.8112 (mt) REVERT: B 135 LYS cc_start: 0.6779 (mtmt) cc_final: 0.6089 (ttpp) REVERT: B 347 CYS cc_start: 0.8143 (m) cc_final: 0.7770 (p) REVERT: B 525 LYS cc_start: 0.7301 (tttp) cc_final: 0.6278 (pmtt) REVERT: B 558 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7254 (ttpt) REVERT: C 293 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7653 (mp) outliers start: 38 outliers final: 17 residues processed: 136 average time/residue: 0.9574 time to fit residues: 142.0497 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.221 Angle : 0.526 7.953 12357 Z= 0.261 Chirality : 0.037 0.131 1393 Planarity : 0.004 0.061 1577 Dihedral : 4.359 59.999 1201 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.78 % Allowed : 14.20 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.29 (0.26), residues: 1093 helix: 1.58 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.015 0.002 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.003 0.000 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.958 Fit side-chains REVERT: A 33 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7956 (tm-30) REVERT: A 34 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6438 (t-90) REVERT: A 77 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 360 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6500 (tm-30) REVERT: A 617 MET cc_start: 0.4571 (pmm) cc_final: 0.2368 (ttm) REVERT: B 63 ILE cc_start: 0.8262 (mm) cc_final: 0.8051 (mt) REVERT: B 135 LYS cc_start: 0.6658 (mtmt) cc_final: 0.5987 (ttpp) REVERT: B 347 CYS cc_start: 0.8132 (m) cc_final: 0.7797 (p) REVERT: B 525 LYS cc_start: 0.7353 (tttp) cc_final: 0.6347 (pmtt) REVERT: B 558 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7230 (ttpt) REVERT: C 293 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7590 (mp) outliers start: 37 outliers final: 13 residues processed: 130 average time/residue: 1.0418 time to fit residues: 148.6573 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9137 Z= 0.212 Angle : 0.528 7.702 12357 Z= 0.262 Chirality : 0.037 0.131 1393 Planarity : 0.004 0.058 1577 Dihedral : 3.960 22.667 1199 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.17 % Allowed : 15.22 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.41 (0.26), residues: 1093 helix: 1.70 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.014 0.002 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.986 Fit side-chains REVERT: A 34 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6487 (t-90) REVERT: A 42 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6985 (tp30) REVERT: A 77 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 360 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6452 (tm-30) REVERT: A 362 ASP cc_start: 0.6394 (OUTLIER) cc_final: 0.5432 (p0) REVERT: A 617 MET cc_start: 0.4690 (pmm) cc_final: 0.2397 (ttm) REVERT: B 63 ILE cc_start: 0.8266 (mm) cc_final: 0.8057 (mt) REVERT: B 344 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7847 (ttm170) REVERT: B 347 CYS cc_start: 0.8120 (m) cc_final: 0.7762 (p) REVERT: B 525 LYS cc_start: 0.7334 (tttp) cc_final: 0.6349 (pmtt) REVERT: B 558 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7133 (ttpt) REVERT: C 293 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7595 (mp) outliers start: 31 outliers final: 17 residues processed: 118 average time/residue: 0.9843 time to fit residues: 126.6873 Evaluate side-chains 117 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8798 > 50: distance: 27 - 34: 5.650 distance: 34 - 35: 3.097 distance: 35 - 36: 3.873 distance: 35 - 38: 9.070 distance: 36 - 43: 6.155 distance: 38 - 39: 8.767 distance: 39 - 40: 7.217 distance: 40 - 41: 4.598 distance: 41 - 42: 18.053 distance: 43 - 44: 7.712 distance: 44 - 45: 6.869 distance: 44 - 47: 3.793 distance: 45 - 46: 5.455 distance: 45 - 54: 8.261 distance: 47 - 48: 7.856 distance: 48 - 49: 8.010 distance: 49 - 50: 4.775 distance: 50 - 51: 14.140 distance: 51 - 53: 10.755 distance: 55 - 56: 4.311 distance: 55 - 58: 9.015 distance: 56 - 57: 7.721 distance: 58 - 59: 9.356 distance: 59 - 60: 10.694 distance: 59 - 61: 8.772 distance: 62 - 63: 7.463 distance: 63 - 64: 9.581 distance: 63 - 66: 7.294 distance: 64 - 65: 14.187 distance: 64 - 70: 9.184 distance: 66 - 67: 7.473 distance: 66 - 68: 14.482 distance: 67 - 69: 9.991 distance: 70 - 71: 21.044 distance: 71 - 72: 16.746 distance: 71 - 74: 21.360 distance: 72 - 73: 5.847 distance: 72 - 78: 14.878 distance: 74 - 75: 12.575 distance: 75 - 76: 16.761 distance: 75 - 77: 18.161 distance: 78 - 79: 8.780 distance: 79 - 80: 8.479 distance: 79 - 82: 14.673 distance: 80 - 81: 7.125 distance: 80 - 86: 8.080 distance: 82 - 83: 13.615 distance: 83 - 84: 5.873 distance: 84 - 85: 22.297 distance: 86 - 87: 12.819 distance: 87 - 88: 13.090 distance: 87 - 90: 9.467 distance: 88 - 89: 6.980 distance: 88 - 94: 5.375 distance: 90 - 91: 5.461 distance: 91 - 92: 7.438 distance: 94 - 95: 10.809 distance: 95 - 96: 10.170 distance: 95 - 98: 9.384 distance: 96 - 97: 19.286 distance: 96 - 105: 19.264 distance: 98 - 99: 16.385 distance: 99 - 100: 6.439 distance: 100 - 101: 13.453 distance: 101 - 102: 8.554 distance: 102 - 103: 3.053 distance: 102 - 104: 7.335 distance: 105 - 106: 17.807 distance: 106 - 107: 23.649 distance: 106 - 109: 44.634 distance: 107 - 108: 17.759 distance: 107 - 113: 29.810 distance: 109 - 110: 14.100 distance: 109 - 111: 20.018 distance: 113 - 114: 5.348 distance: 114 - 115: 13.802 distance: 114 - 117: 7.681 distance: 115 - 116: 16.380 distance: 115 - 121: 11.520 distance: 117 - 118: 18.909 distance: 118 - 119: 8.270 distance: 118 - 120: 13.791