Starting phenix.real_space_refine on Sun Mar 10 21:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7awa_11928/03_2024/7awa_11928.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1667 2.51 5 N 451 2.21 5 O 477 1.98 5 H 2703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 527": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 660": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5310 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Time building chain proxies: 2.90, per 1000 atoms: 0.55 Number of scatterers: 5310 At special positions: 0 Unit cell: (69.12, 74.52, 73.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 477 8.00 N 451 7.00 C 1667 6.00 H 2703 1.00 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: 3.91 Conformation dependent library (CDL) restraints added in 667.0 milliseconds 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 622 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 53.7% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 359 through 362 removed outlier: 3.710A pdb=" N HIS A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.757A pdb=" N ASP A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 379 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 440 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.634A pdb=" N SER A 469 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.727A pdb=" N GLU A 482 " --> pdb=" O HIS A 479 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 484 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 497 removed outlier: 3.869A pdb=" N ARG A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 497 " --> pdb=" O MET A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.776A pdb=" N GLU A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.520A pdb=" N ILE A 516 " --> pdb=" O PRO A 512 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 526 " --> pdb=" O ARG A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.605A pdb=" N ILE A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.869A pdb=" N GLU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 removed outlier: 4.567A pdb=" N ARG A 568 " --> pdb=" O HIS A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 574 removed outlier: 3.723A pdb=" N LYS A 574 " --> pdb=" O PRO A 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 574' Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.924A pdb=" N ARG A 594 " --> pdb=" O ARG A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 621 removed outlier: 5.242A pdb=" N GLN A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 392 removed outlier: 6.997A pdb=" N LEU A 353 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLU A 391 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 355 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 410 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 404 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AA3, first strand: chain 'A' and resid 576 through 578 105 hydrogen bonds defined for protein. 306 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: 1.83 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 2700 1.03 - 1.23: 8 1.23 - 1.42: 1034 1.42 - 1.62: 1591 1.62 - 1.81: 21 Bond restraints: 5354 Sorted by residual: bond pdb=" N SER A 345 " pdb=" H SER A 345 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" N VAL A 347 " pdb=" CA VAL A 347 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.05e-02 9.07e+03 6.40e+00 bond pdb=" N MET A 346 " pdb=" H MET A 346 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" N VAL A 347 " pdb=" H VAL A 347 " ideal model delta sigma weight residual 0.860 0.908 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" C VAL A 347 " pdb=" N PRO A 348 " ideal model delta sigma weight residual 1.331 1.356 -0.026 1.31e-02 5.83e+03 3.79e+00 ... (remaining 5349 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.22: 180 107.22 - 113.89: 6606 113.89 - 120.57: 1666 120.57 - 127.24: 1261 127.24 - 133.92: 27 Bond angle restraints: 9740 Sorted by residual: angle pdb=" CA PRO A 348 " pdb=" C PRO A 348 " pdb=" O PRO A 348 " ideal model delta sigma weight residual 121.67 116.09 5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" CA PRO A 348 " pdb=" C PRO A 348 " pdb=" N GLY A 349 " ideal model delta sigma weight residual 115.16 119.79 -4.63 1.28e+00 6.10e-01 1.31e+01 angle pdb=" CA VAL A 347 " pdb=" C VAL A 347 " pdb=" O VAL A 347 " ideal model delta sigma weight residual 119.62 117.33 2.29 9.00e-01 1.23e+00 6.46e+00 angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.30 113.69 -3.39 1.54e+00 4.22e-01 4.84e+00 angle pdb=" CA VAL A 409 " pdb=" C VAL A 409 " pdb=" N PHE A 410 " ideal model delta sigma weight residual 116.60 119.77 -3.17 1.45e+00 4.76e-01 4.77e+00 ... (remaining 9735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 2224 17.81 - 35.62: 188 35.62 - 53.43: 49 53.43 - 71.24: 14 71.24 - 89.05: 3 Dihedral angle restraints: 2478 sinusoidal: 1410 harmonic: 1068 Sorted by residual: dihedral pdb=" CA ALA A 624 " pdb=" C ALA A 624 " pdb=" N LYS A 625 " pdb=" CA LYS A 625 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG A 607 " pdb=" C ARG A 607 " pdb=" N HIS A 608 " pdb=" CA HIS A 608 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA ARG A 563 " pdb=" CB ARG A 563 " pdb=" CG ARG A 563 " pdb=" CD ARG A 563 " ideal model delta sinusoidal sigma weight residual -60.00 -118.89 58.89 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 274 0.031 - 0.062: 99 0.062 - 0.093: 29 0.093 - 0.124: 22 0.124 - 0.155: 3 Chirality restraints: 427 Sorted by residual: chirality pdb=" CB VAL A 347 " pdb=" CA VAL A 347 " pdb=" CG1 VAL A 347 " pdb=" CG2 VAL A 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CA VAL A 347 " pdb=" N VAL A 347 " pdb=" C VAL A 347 " pdb=" CB VAL A 347 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A 651 " pdb=" N ILE A 651 " pdb=" C ILE A 651 " pdb=" CB ILE A 651 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 424 not shown) Planarity restraints: 767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 371 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ASP A 371 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP A 371 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 395 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.97e+00 pdb=" N PRO A 396 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 649 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 650 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 650 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 650 " -0.016 5.00e-02 4.00e+02 ... (remaining 764 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 607 2.24 - 2.83: 11947 2.83 - 3.42: 12807 3.42 - 4.01: 17007 4.01 - 4.60: 26376 Nonbonded interactions: 68744 Sorted by model distance: nonbonded pdb=" HE ARG A 356 " pdb=" OE1 GLU A 391 " model vdw 1.656 1.850 nonbonded pdb=" O LEU A 355 " pdb=" H GLU A 391 " model vdw 1.664 1.850 nonbonded pdb=" O LEU A 476 " pdb=" H HIS A 479 " model vdw 1.680 1.850 nonbonded pdb=" O THR A 642 " pdb=" H THR A 645 " model vdw 1.723 1.850 nonbonded pdb=" OE1 GLU A 656 " pdb=" H GLU A 656 " model vdw 1.738 1.850 ... (remaining 68739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.080 Extract box with map and model: 5.630 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.460 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2651 Z= 0.218 Angle : 0.637 6.660 3592 Z= 0.380 Chirality : 0.042 0.155 427 Planarity : 0.004 0.035 456 Dihedral : 14.223 89.047 1016 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -2.52 (0.43), residues: 326 helix: -0.95 (0.42), residues: 140 sheet: -1.81 (0.75), residues: 35 loop : -2.32 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 445 HIS 0.001 0.000 HIS A 362 PHE 0.007 0.001 PHE A 483 TYR 0.012 0.002 TYR A 420 ARG 0.006 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.434 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.4978 time to fit residues: 10.5566 Evaluate side-chains 16 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2651 Z= 0.240 Angle : 0.555 5.255 3592 Z= 0.291 Chirality : 0.041 0.137 427 Planarity : 0.004 0.038 456 Dihedral : 5.123 21.343 357 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.43), residues: 326 helix: -0.56 (0.42), residues: 145 sheet: -1.81 (0.72), residues: 35 loop : -2.56 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 543 HIS 0.001 0.000 HIS A 564 PHE 0.009 0.001 PHE A 637 TYR 0.008 0.001 TYR A 420 ARG 0.002 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 16 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.452 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.5071 time to fit residues: 9.6154 Evaluate side-chains 15 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 29 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2651 Z= 0.236 Angle : 0.537 4.614 3592 Z= 0.280 Chirality : 0.041 0.133 427 Planarity : 0.004 0.037 456 Dihedral : 5.027 21.139 357 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.34 % Allowed : 6.19 % Favored : 93.47 % 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: -2.11 (0.44), residues: 326 helix: -0.24 (0.44), residues: 145 sheet: -1.88 (0.69), residues: 37 loop : -2.49 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 445 HIS 0.002 0.000 HIS A 564 PHE 0.006 0.001 PHE A 483 TYR 0.009 0.001 TYR A 420 ARG 0.002 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5703 (tpt) cc_final: 0.5171 (tpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.6376 time to fit residues: 13.1132 Evaluate side-chains 16 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2651 Z= 0.253 Angle : 0.530 4.610 3592 Z= 0.277 Chirality : 0.041 0.136 427 Planarity : 0.004 0.035 456 Dihedral : 4.970 20.140 357 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.34 % Allowed : 6.87 % Favored : 92.78 % 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: -2.02 (0.44), residues: 326 helix: -0.14 (0.44), residues: 145 sheet: -1.65 (0.71), residues: 35 loop : -2.53 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 654 HIS 0.001 0.000 HIS A 564 PHE 0.007 0.001 PHE A 483 TYR 0.010 0.001 TYR A 420 ARG 0.002 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5685 (tpt) cc_final: 0.5471 (tpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4774 time to fit residues: 10.2185 Evaluate side-chains 17 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2651 Z= 0.150 Angle : 0.487 3.674 3592 Z= 0.251 Chirality : 0.040 0.137 427 Planarity : 0.004 0.035 456 Dihedral : 4.731 19.122 357 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.34 % Allowed : 7.22 % Favored : 92.44 % 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: -1.72 (0.45), residues: 326 helix: 0.13 (0.45), residues: 145 sheet: -1.59 (0.70), residues: 35 loop : -2.38 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 445 HIS 0.001 0.000 HIS A 564 PHE 0.005 0.001 PHE A 457 TYR 0.007 0.001 TYR A 420 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4772 time to fit residues: 10.2044 Evaluate side-chains 16 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2651 Z= 0.180 Angle : 0.494 4.082 3592 Z= 0.255 Chirality : 0.040 0.135 427 Planarity : 0.004 0.035 456 Dihedral : 4.639 18.893 357 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.69 % Allowed : 8.25 % Favored : 91.07 % 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: -1.55 (0.45), residues: 326 helix: 0.30 (0.45), residues: 145 sheet: -1.50 (0.71), residues: 35 loop : -2.33 (0.46), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 654 HIS 0.001 0.000 HIS A 564 PHE 0.005 0.001 PHE A 457 TYR 0.008 0.001 TYR A 420 ARG 0.002 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5622 (tpt) cc_final: 0.5105 (tpt) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.4673 time to fit residues: 9.9415 Evaluate side-chains 17 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.013 2651 Z= 0.120 Angle : 0.465 4.449 3592 Z= 0.237 Chirality : 0.039 0.140 427 Planarity : 0.003 0.033 456 Dihedral : 4.420 17.768 357 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 8.25 % Favored : 91.41 % 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: -1.19 (0.46), residues: 326 helix: 0.57 (0.45), residues: 145 sheet: -0.95 (0.76), residues: 28 loop : -2.16 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 445 HIS 0.001 0.000 HIS A 452 PHE 0.005 0.001 PHE A 457 TYR 0.012 0.001 TYR A 420 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5489 (tpt) cc_final: 0.5035 (tpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4832 time to fit residues: 10.3025 Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2651 Z= 0.158 Angle : 0.472 4.496 3592 Z= 0.242 Chirality : 0.040 0.134 427 Planarity : 0.003 0.031 456 Dihedral : 4.374 18.049 357 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.34 % Allowed : 8.93 % Favored : 90.72 % 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: -1.05 (0.46), residues: 326 helix: 0.71 (0.45), residues: 146 sheet: -0.95 (0.77), residues: 28 loop : -2.13 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 654 HIS 0.001 0.000 HIS A 479 PHE 0.004 0.001 PHE A 457 TYR 0.009 0.001 TYR A 420 ARG 0.002 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5690 (tpt) cc_final: 0.5224 (tpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4718 time to fit residues: 10.0844 Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2651 Z= 0.173 Angle : 0.478 5.093 3592 Z= 0.245 Chirality : 0.040 0.133 427 Planarity : 0.003 0.031 456 Dihedral : 4.369 17.575 357 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.34 % Allowed : 8.93 % Favored : 90.72 % 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: -0.98 (0.47), residues: 326 helix: 0.72 (0.45), residues: 147 sheet: -0.86 (0.77), residues: 28 loop : -2.06 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 654 HIS 0.001 0.000 HIS A 452 PHE 0.005 0.001 PHE A 483 TYR 0.011 0.001 TYR A 420 ARG 0.001 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5597 (tpt) cc_final: 0.5158 (tpt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4803 time to fit residues: 10.3077 Evaluate side-chains 18 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2651 Z= 0.122 Angle : 0.460 5.589 3592 Z= 0.232 Chirality : 0.039 0.137 427 Planarity : 0.003 0.031 456 Dihedral : 4.162 16.612 357 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 8.93 % Favored : 90.72 % 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: -0.76 (0.47), residues: 326 helix: 0.90 (0.46), residues: 148 sheet: -0.79 (0.79), residues: 28 loop : -1.94 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 445 HIS 0.001 0.000 HIS A 564 PHE 0.004 0.001 PHE A 457 TYR 0.009 0.001 TYR A 420 ARG 0.001 0.000 ARG A 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 652 Ramachandran restraints generated. 326 Oldfield, 0 Emsley, 326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 579 is missing expected H atoms. Skipping. Evaluate side-chains 19 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 598 MET cc_start: 0.5689 (tpt) cc_final: 0.5281 (tpt) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.4516 time to fit residues: 10.1973 Evaluate side-chains 19 residues out of total 291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065851 restraints weight = 21053.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069068 restraints weight = 9360.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070938 restraints weight = 6221.641| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2651 Z= 0.146 Angle : 0.466 5.269 3592 Z= 0.237 Chirality : 0.039 0.136 427 Planarity : 0.003 0.030 456 Dihedral : 4.161 16.804 357 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.34 % Allowed : 9.28 % Favored : 90.38 % 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: -0.74 (0.47), residues: 326 helix: 0.90 (0.46), residues: 148 sheet: -0.61 (0.80), residues: 28 loop : -1.95 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 654 HIS 0.001 0.000 HIS A 479 PHE 0.004 0.001 PHE A 457 TYR 0.009 0.001 TYR A 420 ARG 0.002 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.09 seconds wall clock time: 35 minutes 32.55 seconds (2132.55 seconds total)