Starting phenix.real_space_refine on Thu Jul 18 23:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqs_25392/07_2024/7sqs_25392.cif" } resolution = 3.1 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= 0.010 sd= 0.044 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 14 5.16 5 C 2730 2.51 5 N 789 2.21 5 O 843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4376 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3970 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 23, 'TRANS': 484} Chain breaks: 1 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Time building chain proxies: 3.52, per 1000 atoms: 0.80 Number of scatterers: 4376 At special positions: 0 Unit cell: (78.4536, 68.9851, 86.5695, 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 14 16.00 O 843 8.00 N 789 7.00 C 2730 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: 1.39 Conformation dependent library (CDL) restraints added in 820.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 40.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.770A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.021A pdb=" N LYS A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.660A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.971A pdb=" N ALA A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.699A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.704A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.620A pdb=" N ARG A 465 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.855A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.720A pdb=" N GLN A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.568A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.676A pdb=" N ASN B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.949A pdb=" N GLU A 476 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR A 559 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 478 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N CYS A 557 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN A 480 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU A 555 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 482 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS A 553 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 331 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 332 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN A 292 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 291 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 270 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 243 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 195 hydrogen bonds defined for protein. 501 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: 1.20 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1527 1.34 - 1.46: 761 1.46 - 1.57: 2141 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4455 Sorted by residual: bond pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 9.81e-01 bond pdb=" N GLN A 238 " pdb=" CA GLN A 238 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.47e-01 bond pdb=" CB GLN A 278 " pdb=" CG GLN A 278 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.27e-01 bond pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 8.14e-01 bond pdb=" N TYR A 543 " pdb=" CA TYR A 543 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.22e-02 6.72e+03 6.59e-01 ... (remaining 4450 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 122 106.93 - 113.71: 2389 113.71 - 120.49: 1686 120.49 - 127.26: 1793 127.26 - 134.04: 46 Bond angle restraints: 6036 Sorted by residual: angle pdb=" N ASP A 375 " pdb=" CA ASP A 375 " pdb=" C ASP A 375 " ideal model delta sigma weight residual 113.56 109.64 3.92 1.39e+00 5.18e-01 7.94e+00 angle pdb=" CA GLN A 278 " pdb=" CB GLN A 278 " pdb=" CG GLN A 278 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.41e+00 angle pdb=" C THR A 286 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " ideal model delta sigma weight residual 122.46 125.41 -2.95 1.41e+00 5.03e-01 4.38e+00 angle pdb=" C GLN A 278 " pdb=" CA GLN A 278 " pdb=" CB GLN A 278 " ideal model delta sigma weight residual 111.91 114.82 -2.91 1.52e+00 4.33e-01 3.67e+00 angle pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " pdb=" CG ASP A 287 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.62e+00 ... (remaining 6031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 2405 17.07 - 34.14: 223 34.14 - 51.20: 34 51.20 - 68.27: 6 68.27 - 85.34: 6 Dihedral angle restraints: 2674 sinusoidal: 1075 harmonic: 1599 Sorted by residual: dihedral pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.92 51.92 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA MET A 385 " pdb=" CB MET A 385 " pdb=" CG MET A 385 " pdb=" SD MET A 385 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 3 1.50e+01 4.44e-03 8.03e+00 dihedral pdb=" CB ARG A 497 " pdb=" CG ARG A 497 " pdb=" CD ARG A 497 " pdb=" NE ARG A 497 " ideal model delta sinusoidal sigma weight residual -60.00 -101.07 41.07 3 1.50e+01 4.44e-03 7.34e+00 ... (remaining 2671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 415 0.028 - 0.055: 154 0.055 - 0.083: 41 0.083 - 0.111: 40 0.111 - 0.138: 12 Chirality restraints: 662 Sorted by residual: chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 659 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 320 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 528 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.67e-01 pdb=" N PRO A 529 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 287 " 0.005 2.00e-02 2.50e+03 9.39e-03 8.82e-01 pdb=" C ASP A 287 " -0.016 2.00e-02 2.50e+03 pdb=" O ASP A 287 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL A 288 " 0.005 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1388 2.83 - 3.35: 3878 3.35 - 3.87: 6531 3.87 - 4.38: 7051 4.38 - 4.90: 13013 Nonbonded interactions: 31861 Sorted by model distance: nonbonded pdb=" O TRP A 384 " pdb=" NH2 ARG A 389 " model vdw 2.317 2.520 nonbonded pdb=" O ASN A 524 " pdb=" NH1 ARG A 532 " model vdw 2.324 2.520 nonbonded pdb=" OE2 GLU A 514 " pdb=" OH TYR A 543 " model vdw 2.335 2.440 nonbonded pdb=" NE2 GLN A 175 " pdb=" O ALA A 183 " model vdw 2.353 2.520 nonbonded pdb=" OD1 ASP A 219 " pdb=" NE ARG E 56 " model vdw 2.375 2.520 ... (remaining 31856 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: 1.400 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.002 0.029 4455 Z= 0.128 Angle : 0.469 6.258 6036 Z= 0.259 Chirality : 0.040 0.138 662 Planarity : 0.003 0.050 813 Dihedral : 13.610 85.335 1642 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.38), residues: 548 helix: 2.17 (0.40), residues: 185 sheet: 0.50 (0.47), residues: 130 loop : -0.42 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.001 0.000 HIS A 101 PHE 0.004 0.001 PHE A 399 TYR 0.004 0.001 TYR A 166 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.525 Fit side-chains REVERT: A 388 LEU cc_start: 0.8923 (pt) cc_final: 0.8640 (mm) REVERT: A 491 ASP cc_start: 0.8299 (t0) cc_final: 0.8056 (t0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1658 time to fit residues: 11.6190 Evaluate side-chains 43 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 622 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4455 Z= 0.172 Angle : 0.466 7.850 6036 Z= 0.248 Chirality : 0.042 0.153 662 Planarity : 0.003 0.046 813 Dihedral : 3.331 13.502 602 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.43 % Allowed : 4.74 % Favored : 94.83 % 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: 1.04 (0.38), residues: 548 helix: 2.27 (0.40), residues: 191 sheet: 0.25 (0.46), residues: 129 loop : -0.37 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.001 0.001 HIS A 224 PHE 0.023 0.001 PHE A 283 TYR 0.007 0.001 TYR A 570 ARG 0.001 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.404 Fit side-chains REVERT: A 248 ASP cc_start: 0.8423 (t0) cc_final: 0.8029 (t0) REVERT: A 388 LEU cc_start: 0.8862 (pt) cc_final: 0.8610 (mm) REVERT: A 491 ASP cc_start: 0.8328 (t0) cc_final: 0.8096 (t0) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.1297 time to fit residues: 8.4706 Evaluate side-chains 43 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 281 ASN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4455 Z= 0.210 Angle : 0.480 6.302 6036 Z= 0.254 Chirality : 0.042 0.151 662 Planarity : 0.003 0.043 813 Dihedral : 3.482 13.141 602 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 6.25 % Favored : 92.24 % 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: 0.96 (0.38), residues: 548 helix: 2.20 (0.40), residues: 192 sheet: 0.15 (0.46), residues: 129 loop : -0.39 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.002 0.001 HIS A 224 PHE 0.011 0.001 PHE A 399 TYR 0.007 0.001 TYR A 519 ARG 0.002 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.549 Fit side-chains REVERT: A 248 ASP cc_start: 0.8363 (t0) cc_final: 0.7997 (t0) REVERT: A 283 PHE cc_start: 0.7984 (m-80) cc_final: 0.7761 (m-80) outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 0.1395 time to fit residues: 9.5234 Evaluate side-chains 47 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4455 Z= 0.267 Angle : 0.509 5.786 6036 Z= 0.267 Chirality : 0.043 0.155 662 Planarity : 0.004 0.040 813 Dihedral : 3.715 14.302 602 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.29 % Allowed : 7.76 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.37), residues: 548 helix: 2.16 (0.40), residues: 188 sheet: 0.09 (0.46), residues: 129 loop : -0.45 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 487 HIS 0.002 0.001 HIS A 224 PHE 0.010 0.001 PHE A 399 TYR 0.009 0.001 TYR A 519 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 147 MET cc_start: 0.4201 (pmm) cc_final: 0.1950 (ptp) REVERT: A 248 ASP cc_start: 0.8371 (t0) cc_final: 0.8012 (t0) REVERT: A 283 PHE cc_start: 0.8054 (m-80) cc_final: 0.7824 (m-80) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1498 time to fit residues: 9.5249 Evaluate side-chains 45 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4455 Z= 0.140 Angle : 0.462 6.689 6036 Z= 0.239 Chirality : 0.041 0.150 662 Planarity : 0.003 0.037 813 Dihedral : 3.371 12.607 602 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.29 % Allowed : 9.48 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.38), residues: 548 helix: 2.35 (0.40), residues: 188 sheet: 0.21 (0.46), residues: 129 loop : -0.39 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 105 HIS 0.002 0.000 HIS A 358 PHE 0.011 0.001 PHE A 296 TYR 0.005 0.001 TYR A 166 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.539 Fit side-chains REVERT: A 248 ASP cc_start: 0.8322 (t0) cc_final: 0.7930 (t0) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.1360 time to fit residues: 8.7228 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4455 Z= 0.220 Angle : 0.486 6.271 6036 Z= 0.254 Chirality : 0.042 0.152 662 Planarity : 0.003 0.035 813 Dihedral : 3.538 13.678 602 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.94 % Allowed : 8.84 % Favored : 89.22 % 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: 0.93 (0.38), residues: 548 helix: 2.29 (0.40), residues: 187 sheet: 0.19 (0.46), residues: 129 loop : -0.49 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.002 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.006 0.001 TYR A 519 ARG 0.002 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.550 Fit side-chains REVERT: A 248 ASP cc_start: 0.8342 (t0) cc_final: 0.7948 (t0) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.1575 time to fit residues: 10.1852 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4455 Z= 0.145 Angle : 0.474 7.091 6036 Z= 0.241 Chirality : 0.041 0.150 662 Planarity : 0.003 0.033 813 Dihedral : 3.334 12.501 602 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.94 % Allowed : 9.91 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.38), residues: 548 helix: 2.36 (0.40), residues: 188 sheet: 0.25 (0.46), residues: 129 loop : -0.42 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 105 HIS 0.001 0.000 HIS A 358 PHE 0.010 0.001 PHE A 296 TYR 0.005 0.001 TYR A 166 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.531 Fit side-chains REVERT: A 248 ASP cc_start: 0.8312 (t0) cc_final: 0.7906 (t0) REVERT: A 283 PHE cc_start: 0.7914 (m-80) cc_final: 0.7681 (m-80) outliers start: 9 outliers final: 8 residues processed: 48 average time/residue: 0.1537 time to fit residues: 9.9119 Evaluate side-chains 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.0060 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.4894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4455 Z= 0.165 Angle : 0.475 6.983 6036 Z= 0.243 Chirality : 0.041 0.149 662 Planarity : 0.003 0.033 813 Dihedral : 3.326 12.295 602 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.51 % Allowed : 10.34 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.38), residues: 548 helix: 2.36 (0.40), residues: 188 sheet: 0.22 (0.46), residues: 129 loop : -0.42 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR A 519 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.573 Fit side-chains REVERT: A 283 PHE cc_start: 0.7919 (m-80) cc_final: 0.7681 (m-80) outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.1356 time to fit residues: 8.7945 Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4455 Z= 0.134 Angle : 0.485 10.200 6036 Z= 0.249 Chirality : 0.041 0.148 662 Planarity : 0.003 0.032 813 Dihedral : 3.180 11.994 602 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.08 % Allowed : 10.56 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.38), residues: 548 helix: 2.44 (0.40), residues: 188 sheet: 0.28 (0.46), residues: 129 loop : -0.35 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 358 PHE 0.009 0.001 PHE A 296 TYR 0.003 0.000 TYR A 519 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.528 Fit side-chains REVERT: A 283 PHE cc_start: 0.7912 (m-80) cc_final: 0.7661 (m-80) outliers start: 5 outliers final: 5 residues processed: 45 average time/residue: 0.1345 time to fit residues: 8.5719 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4455 Z= 0.153 Angle : 0.488 9.078 6036 Z= 0.249 Chirality : 0.041 0.147 662 Planarity : 0.003 0.032 813 Dihedral : 3.207 11.785 602 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.08 % Allowed : 10.99 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.38), residues: 548 helix: 2.40 (0.40), residues: 188 sheet: 0.31 (0.46), residues: 129 loop : -0.39 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.004 0.001 TYR A 519 ARG 0.002 0.000 ARG B 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.532 Fit side-chains REVERT: A 283 PHE cc_start: 0.7912 (m-80) cc_final: 0.7660 (m-80) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.1285 time to fit residues: 8.4645 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069498 restraints weight = 10284.822| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.33 r_work: 0.2958 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4455 Z= 0.170 Angle : 0.492 7.472 6036 Z= 0.252 Chirality : 0.041 0.148 662 Planarity : 0.003 0.032 813 Dihedral : 3.300 12.000 602 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 10.78 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 548 helix: 2.34 (0.40), residues: 188 sheet: 0.28 (0.46), residues: 129 loop : -0.44 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR A 519 ARG 0.002 0.000 ARG B 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1294.24 seconds wall clock time: 23 minutes 34.38 seconds (1414.38 seconds total)