Starting phenix.real_space_refine on Sun Mar 10 22:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yqm_34029/03_2024/7yqm_34029.pdb" } resolution = 2.89 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= 0.001 sd= 0.036 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 29 5.16 5 C 3543 2.51 5 N 1015 2.21 5 O 1069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5656 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5656 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 31, 'TRANS': 691} Time building chain proxies: 3.69, per 1000 atoms: 0.65 Number of scatterers: 5656 At special positions: 0 Unit cell: (76.446, 81.378, 93.708, 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 29 16.00 O 1069 8.00 N 1015 7.00 C 3543 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 53.0% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 31 through 71 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 159 through 178 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 279 through 296 Processing helix chain 'A' and resid 359 through 378 removed outlier: 4.224A pdb=" N TYR A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 414 removed outlier: 4.033A pdb=" N GLU A 398 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 453 through 464 Processing helix chain 'A' and resid 465 through 468 removed outlier: 3.573A pdb=" N GLY A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 465 through 468' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.812A pdb=" N LYS A 477 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 496 removed outlier: 3.604A pdb=" N LYS A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 537 through 551 removed outlier: 4.384A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 548 " --> pdb=" O HIS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 563 through 567 removed outlier: 5.878A pdb=" N ASN A 566 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 567 " --> pdb=" O GLU A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 568 through 577 Processing helix chain 'A' and resid 588 through 613 removed outlier: 4.039A pdb=" N ARG A 609 " --> pdb=" O GLY A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 648 Processing helix chain 'A' and resid 652 through 671 Processing helix chain 'A' and resid 683 through 686 Processing helix chain 'A' and resid 687 through 699 Processing helix chain 'A' and resid 700 through 707 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 708 through 723 removed outlier: 3.540A pdb=" N HIS A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 8.214A pdb=" N VAL A 348 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE A 349 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 503 through 505 removed outlier: 6.809A pdb=" N ALA A 447 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N GLY A 505 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 449 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA A 447 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N MET A 422 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A 449 " --> pdb=" O MET A 422 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 424 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR A 451 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 426 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL A 386 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY A 423 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 388 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A 425 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LYS A 390 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU A 335 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A 389 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 337 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR A 267 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG A 338 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 269 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A 116 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 135 through 137 removed outlier: 3.540A pdb=" N ASP A 258 " --> pdb=" O GLN A 241 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N HIS A 237 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR A 227 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS A 228 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS A 232 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE A 216 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY A 221 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N HIS A 318 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 194 removed outlier: 6.648A pdb=" N GLN A 201 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE A 191 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 199 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL A 193 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA6, first strand: chain 'A' and resid 620 through 621 289 hydrogen bonds defined for protein. 834 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: 1.89 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 983 1.30 - 1.42: 1403 1.42 - 1.55: 3289 1.55 - 1.68: 37 1.68 - 1.81: 52 Bond restraints: 5764 Sorted by residual: bond pdb=" C SER A 437 " pdb=" O SER A 437 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" C GLU A 49 " pdb=" O GLU A 49 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.29e-02 6.01e+03 1.80e+01 bond pdb=" CA ILE A 642 " pdb=" CB ILE A 642 " ideal model delta sigma weight residual 1.540 1.589 -0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" CA THR A 209 " pdb=" CB THR A 209 " ideal model delta sigma weight residual 1.532 1.587 -0.056 1.45e-02 4.76e+03 1.47e+01 bond pdb=" C ILE A 642 " pdb=" O ILE A 642 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.19e-02 7.06e+03 1.05e+01 ... (remaining 5759 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.10: 187 107.10 - 113.83: 3196 113.83 - 120.57: 2255 120.57 - 127.30: 2106 127.30 - 134.04: 68 Bond angle restraints: 7812 Sorted by residual: angle pdb=" N GLU A 49 " pdb=" CA GLU A 49 " pdb=" C GLU A 49 " ideal model delta sigma weight residual 112.23 106.86 5.37 1.26e+00 6.30e-01 1.82e+01 angle pdb=" CA LEU A 491 " pdb=" C LEU A 491 " pdb=" N SER A 492 " ideal model delta sigma weight residual 117.63 122.73 -5.10 1.25e+00 6.40e-01 1.66e+01 angle pdb=" N ASP A 668 " pdb=" CA ASP A 668 " pdb=" C ASP A 668 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.65e+01 angle pdb=" N ILE A 642 " pdb=" CA ILE A 642 " pdb=" CB ILE A 642 " ideal model delta sigma weight residual 110.58 116.35 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C ASP A 668 " pdb=" CA ASP A 668 " pdb=" CB ASP A 668 " ideal model delta sigma weight residual 110.88 104.99 5.89 1.57e+00 4.06e-01 1.41e+01 ... (remaining 7807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3286 16.84 - 33.68: 168 33.68 - 50.51: 26 50.51 - 67.35: 11 67.35 - 84.19: 8 Dihedral angle restraints: 3499 sinusoidal: 1415 harmonic: 2084 Sorted by residual: dihedral pdb=" CA LEU A 343 " pdb=" C LEU A 343 " pdb=" N MET A 344 " pdb=" CA MET A 344 " ideal model delta harmonic sigma weight residual -180.00 -162.90 -17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB MET A 470 " pdb=" CG MET A 470 " pdb=" SD MET A 470 " pdb=" CE MET A 470 " ideal model delta sinusoidal sigma weight residual 60.00 109.11 -49.11 3 1.50e+01 4.44e-03 8.73e+00 dihedral pdb=" CA GLN A 186 " pdb=" CB GLN A 186 " pdb=" CG GLN A 186 " pdb=" CD GLN A 186 " ideal model delta sinusoidal sigma weight residual 180.00 133.88 46.12 3 1.50e+01 4.44e-03 8.28e+00 ... (remaining 3496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 712 0.050 - 0.100: 108 0.100 - 0.150: 35 0.150 - 0.201: 4 0.201 - 0.251: 5 Chirality restraints: 864 Sorted by residual: chirality pdb=" CG LEU A 210 " pdb=" CB LEU A 210 " pdb=" CD1 LEU A 210 " pdb=" CD2 LEU A 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 118 " pdb=" CA VAL A 118 " pdb=" CG1 VAL A 118 " pdb=" CG2 VAL A 118 " both_signs ideal model delta sigma weight residual False -2.63 -2.86 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU A 491 " pdb=" CB LEU A 491 " pdb=" CD1 LEU A 491 " pdb=" CD2 LEU A 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 861 not shown) Planarity restraints: 1034 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 197 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C GLN A 197 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN A 197 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 198 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 490 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.31e+00 pdb=" C VAL A 490 " -0.040 2.00e-02 2.50e+03 pdb=" O VAL A 490 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 491 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 569 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C PHE A 569 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE A 569 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 570 " 0.010 2.00e-02 2.50e+03 ... (remaining 1031 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1550 2.82 - 3.34: 5621 3.34 - 3.86: 9547 3.86 - 4.38: 11823 4.38 - 4.90: 20105 Nonbonded interactions: 48646 Sorted by model distance: nonbonded pdb=" O GLY A 104 " pdb=" OG SER A 385 " model vdw 2.294 2.440 nonbonded pdb=" O PHE A 453 " pdb=" OG1 THR A 457 " model vdw 2.339 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" OG SER A 381 " model vdw 2.341 2.440 nonbonded pdb=" O ASP A 426 " pdb=" OH TYR A 485 " model vdw 2.346 2.440 nonbonded pdb=" OG1 THR A 451 " pdb=" OE1 GLU A 486 " model vdw 2.349 2.440 ... (remaining 48641 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 7.020 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 5764 Z= 0.339 Angle : 0.581 6.059 7812 Z= 0.361 Chirality : 0.045 0.251 864 Planarity : 0.004 0.036 1034 Dihedral : 11.882 84.188 2155 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.17 % Allowed : 0.83 % Favored : 99.00 % 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: -0.02 (0.31), residues: 721 helix: 1.12 (0.28), residues: 352 sheet: -1.77 (0.56), residues: 69 loop : -0.89 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.004 0.001 HIS A 544 PHE 0.008 0.001 PHE A 191 TYR 0.017 0.001 TYR A 485 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.595 Fit side-chains REVERT: A 281 GLU cc_start: 0.6433 (mm-30) cc_final: 0.6061 (mm-30) REVERT: A 570 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6709 (tp30) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 1.4645 time to fit residues: 144.5712 Evaluate side-chains 64 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 378 GLN A 593 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5764 Z= 0.355 Angle : 0.586 7.374 7812 Z= 0.312 Chirality : 0.046 0.148 864 Planarity : 0.005 0.037 1034 Dihedral : 4.356 18.431 784 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.33 % Allowed : 9.50 % Favored : 89.17 % 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: 0.00 (0.31), residues: 721 helix: 1.12 (0.28), residues: 357 sheet: -1.61 (0.56), residues: 71 loop : -0.92 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 169 HIS 0.006 0.001 HIS A 648 PHE 0.011 0.002 PHE A 448 TYR 0.018 0.002 TYR A 485 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.638 Fit side-chains REVERT: A 266 SER cc_start: 0.8862 (p) cc_final: 0.8662 (m) REVERT: A 281 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6115 (mm-30) REVERT: A 629 MET cc_start: 0.8161 (ttp) cc_final: 0.7769 (ttt) REVERT: A 669 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6744 (tt0) outliers start: 8 outliers final: 1 residues processed: 73 average time/residue: 1.3217 time to fit residues: 100.9324 Evaluate side-chains 68 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5764 Z= 0.198 Angle : 0.487 6.422 7812 Z= 0.259 Chirality : 0.041 0.144 864 Planarity : 0.004 0.035 1034 Dihedral : 4.098 17.395 784 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.17 % Allowed : 11.67 % Favored : 87.17 % 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: 0.33 (0.31), residues: 721 helix: 1.39 (0.28), residues: 358 sheet: -1.32 (0.57), residues: 68 loop : -0.82 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.004 0.001 HIS A 648 PHE 0.013 0.001 PHE A 453 TYR 0.015 0.001 TYR A 485 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.630 Fit side-chains REVERT: A 64 LEU cc_start: 0.7757 (tp) cc_final: 0.7550 (tp) REVERT: A 281 GLU cc_start: 0.6292 (mm-30) cc_final: 0.6054 (mm-30) REVERT: A 623 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5407 (tt) REVERT: A 629 MET cc_start: 0.8162 (ttp) cc_final: 0.7847 (ttt) REVERT: A 669 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6717 (tt0) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 1.1784 time to fit residues: 90.4894 Evaluate side-chains 65 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5764 Z= 0.177 Angle : 0.468 6.202 7812 Z= 0.247 Chirality : 0.041 0.135 864 Planarity : 0.004 0.035 1034 Dihedral : 3.982 16.478 784 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.33 % Allowed : 12.17 % Favored : 85.50 % 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: 0.52 (0.31), residues: 721 helix: 1.53 (0.28), residues: 358 sheet: -1.08 (0.59), residues: 68 loop : -0.75 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.004 0.001 HIS A 648 PHE 0.017 0.001 PHE A 453 TYR 0.014 0.001 TYR A 485 ARG 0.003 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.674 Fit side-chains REVERT: A 9 ARG cc_start: 0.7365 (ptt180) cc_final: 0.7060 (ptt90) REVERT: A 97 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6775 (ttp-110) REVERT: A 126 TYR cc_start: 0.7229 (m-10) cc_final: 0.6760 (m-80) REVERT: A 281 GLU cc_start: 0.6292 (mm-30) cc_final: 0.6059 (mm-30) REVERT: A 623 ILE cc_start: 0.5750 (OUTLIER) cc_final: 0.5420 (tt) REVERT: A 629 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (ttt) REVERT: A 669 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6639 (tt0) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 1.1424 time to fit residues: 86.6171 Evaluate side-chains 68 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5764 Z= 0.245 Angle : 0.509 7.822 7812 Z= 0.268 Chirality : 0.042 0.137 864 Planarity : 0.004 0.036 1034 Dihedral : 4.100 16.919 784 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.67 % Allowed : 13.33 % Favored : 84.00 % 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: 0.43 (0.31), residues: 721 helix: 1.43 (0.28), residues: 358 sheet: -0.91 (0.60), residues: 68 loop : -0.81 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 169 HIS 0.004 0.001 HIS A 648 PHE 0.009 0.001 PHE A 495 TYR 0.015 0.001 TYR A 485 ARG 0.002 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.664 Fit side-chains REVERT: A 97 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6985 (ttp-110) REVERT: A 126 TYR cc_start: 0.7235 (m-10) cc_final: 0.6783 (m-80) REVERT: A 281 GLU cc_start: 0.6354 (mm-30) cc_final: 0.6104 (mm-30) REVERT: A 623 ILE cc_start: 0.5779 (OUTLIER) cc_final: 0.5400 (tt) REVERT: A 629 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7878 (ttt) REVERT: A 669 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6735 (tt0) outliers start: 16 outliers final: 5 residues processed: 72 average time/residue: 1.2039 time to fit residues: 91.3344 Evaluate side-chains 70 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.0060 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5764 Z= 0.187 Angle : 0.465 5.339 7812 Z= 0.247 Chirality : 0.041 0.136 864 Planarity : 0.004 0.035 1034 Dihedral : 3.976 16.349 784 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.00 % Allowed : 14.50 % Favored : 83.50 % 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: 0.58 (0.31), residues: 721 helix: 1.58 (0.28), residues: 358 sheet: -0.83 (0.61), residues: 68 loop : -0.78 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 169 HIS 0.004 0.001 HIS A 648 PHE 0.010 0.001 PHE A 495 TYR 0.015 0.001 TYR A 485 ARG 0.002 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.623 Fit side-chains REVERT: A 97 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6910 (ttp-110) REVERT: A 126 TYR cc_start: 0.7193 (m-10) cc_final: 0.6745 (m-80) REVERT: A 281 GLU cc_start: 0.6313 (mm-30) cc_final: 0.6074 (mm-30) REVERT: A 465 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7603 (ttm) REVERT: A 623 ILE cc_start: 0.5813 (OUTLIER) cc_final: 0.5476 (tt) REVERT: A 629 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (ttt) REVERT: A 669 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6640 (tt0) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 1.1769 time to fit residues: 85.3962 Evaluate side-chains 73 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 97 ARG Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 58 optimal weight: 0.0010 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5764 Z= 0.149 Angle : 0.458 8.575 7812 Z= 0.239 Chirality : 0.040 0.134 864 Planarity : 0.003 0.033 1034 Dihedral : 3.831 15.471 784 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.50 % Allowed : 15.33 % Favored : 83.17 % 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: 0.73 (0.32), residues: 721 helix: 1.75 (0.28), residues: 358 sheet: -0.93 (0.65), residues: 63 loop : -0.74 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 481 HIS 0.003 0.001 HIS A 462 PHE 0.010 0.001 PHE A 495 TYR 0.014 0.001 TYR A 485 ARG 0.002 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.622 Fit side-chains REVERT: A 126 TYR cc_start: 0.7233 (m-10) cc_final: 0.6804 (m-80) REVERT: A 154 MET cc_start: 0.7582 (tpt) cc_final: 0.7363 (tpt) REVERT: A 281 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6056 (mm-30) REVERT: A 465 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (ttm) REVERT: A 486 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 623 ILE cc_start: 0.5666 (OUTLIER) cc_final: 0.5323 (tt) REVERT: A 629 MET cc_start: 0.8098 (ttp) cc_final: 0.7779 (ttt) REVERT: A 669 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6615 (tt0) outliers start: 9 outliers final: 4 residues processed: 71 average time/residue: 1.1305 time to fit residues: 84.5034 Evaluate side-chains 71 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5764 Z= 0.194 Angle : 0.469 5.166 7812 Z= 0.248 Chirality : 0.041 0.135 864 Planarity : 0.004 0.034 1034 Dihedral : 3.902 15.748 784 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.33 % Allowed : 15.00 % Favored : 82.67 % 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: 0.63 (0.31), residues: 721 helix: 1.67 (0.28), residues: 358 sheet: -0.92 (0.65), residues: 63 loop : -0.80 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 169 HIS 0.004 0.001 HIS A 648 PHE 0.009 0.001 PHE A 495 TYR 0.014 0.001 TYR A 485 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.637 Fit side-chains REVERT: A 12 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5312 (mp) REVERT: A 126 TYR cc_start: 0.7216 (m-10) cc_final: 0.6784 (m-80) REVERT: A 281 GLU cc_start: 0.6305 (mm-30) cc_final: 0.6067 (mm-30) REVERT: A 465 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7557 (ttm) REVERT: A 486 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 623 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5489 (tt) REVERT: A 629 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7781 (ttt) REVERT: A 669 GLN cc_start: 0.7184 (OUTLIER) cc_final: 0.6680 (tt0) outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 1.1762 time to fit residues: 85.4058 Evaluate side-chains 75 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0570 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5764 Z= 0.131 Angle : 0.449 8.770 7812 Z= 0.233 Chirality : 0.039 0.133 864 Planarity : 0.003 0.033 1034 Dihedral : 3.723 14.916 784 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.50 % Allowed : 16.33 % Favored : 82.17 % 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: 0.83 (0.32), residues: 721 helix: 1.83 (0.28), residues: 359 sheet: -0.95 (0.69), residues: 58 loop : -0.69 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 481 HIS 0.003 0.001 HIS A 462 PHE 0.010 0.001 PHE A 495 TYR 0.013 0.001 TYR A 485 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.655 Fit side-chains REVERT: A 126 TYR cc_start: 0.7247 (m-10) cc_final: 0.6819 (m-80) REVERT: A 281 GLU cc_start: 0.6257 (mm-30) cc_final: 0.6021 (mm-30) REVERT: A 312 LYS cc_start: 0.6219 (ttmt) cc_final: 0.5974 (mtpp) REVERT: A 465 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7565 (ttm) REVERT: A 486 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 623 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5547 (tt) REVERT: A 629 MET cc_start: 0.8082 (ttp) cc_final: 0.7853 (ttt) REVERT: A 669 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6615 (tt0) outliers start: 9 outliers final: 3 residues processed: 71 average time/residue: 1.2465 time to fit residues: 92.9256 Evaluate side-chains 68 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5764 Z= 0.248 Angle : 0.515 6.499 7812 Z= 0.271 Chirality : 0.042 0.138 864 Planarity : 0.004 0.034 1034 Dihedral : 3.978 15.785 784 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.50 % Allowed : 16.83 % Favored : 81.67 % 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: 0.57 (0.31), residues: 721 helix: 1.60 (0.28), residues: 358 sheet: -1.00 (0.68), residues: 58 loop : -0.79 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.005 0.001 HIS A 648 PHE 0.010 0.002 PHE A 453 TYR 0.015 0.001 TYR A 485 ARG 0.004 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1442 Ramachandran restraints generated. 721 Oldfield, 0 Emsley, 721 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.660 Fit side-chains REVERT: A 126 TYR cc_start: 0.7260 (m-10) cc_final: 0.6822 (m-80) REVERT: A 281 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6130 (mm-30) REVERT: A 465 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: A 486 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 623 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5499 (tt) REVERT: A 629 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7749 (ttt) REVERT: A 669 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6693 (tt0) outliers start: 9 outliers final: 4 residues processed: 66 average time/residue: 1.2483 time to fit residues: 86.5005 Evaluate side-chains 70 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 669 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 7 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144597 restraints weight = 6044.903| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.19 r_work: 0.3550 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5764 Z= 0.178 Angle : 0.480 6.787 7812 Z= 0.252 Chirality : 0.041 0.135 864 Planarity : 0.003 0.033 1034 Dihedral : 3.875 15.450 784 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.33 % Allowed : 16.83 % Favored : 81.83 % 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: 0.68 (0.32), residues: 721 helix: 1.69 (0.28), residues: 358 sheet: -0.92 (0.68), residues: 58 loop : -0.75 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 169 HIS 0.003 0.001 HIS A 648 PHE 0.009 0.001 PHE A 495 TYR 0.016 0.001 TYR A 485 ARG 0.003 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.26 seconds wall clock time: 41 minutes 49.17 seconds (2509.17 seconds total)