Starting phenix.real_space_refine on Thu Nov 14 09:36:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tr9_41574/11_2024/8tr9_41574.cif" } resolution = 3.2 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= 0.004 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 P 2 5.49 5 S 30 5.16 5 C 3431 2.51 5 N 937 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5442 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5414 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 32, 'TRANS': 651} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.29, per 1000 atoms: 1.52 Number of scatterers: 5442 At special positions: 0 Unit cell: (55.836, 78.067, 123.563, 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 30 16.00 P 2 15.00 O 1042 8.00 N 937 7.00 C 3431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 850.4 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1268 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 19.0% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 244 through 248 removed outlier: 4.346A pdb=" N ASP A 247 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.767A pdb=" N ILE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 389 through 399 removed outlier: 3.753A pdb=" N VAL A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'A' and resid 547 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 4.300A pdb=" N ARG A 9 " --> pdb=" O HIS A 44 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A 94 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN A 103 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 92 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR A 105 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA A 90 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.462A pdb=" N LEU A 31 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 120 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 removed outlier: 4.462A pdb=" N LEU A 31 " --> pdb=" O HIS A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 375 removed outlier: 3.514A pdb=" N VAL A 374 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 333 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL A 297 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS A 429 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 317 removed outlier: 7.942A pdb=" N VAL A 401 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN A 417 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASP A 403 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 575 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 577 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 560 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 566 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR A 503 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 532 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N CYS A 505 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU A 530 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 507 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR A 528 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 509 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 526 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA A 511 " --> pdb=" O CYS A 524 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 513 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 478 Processing sheet with id=AA9, first strand: chain 'A' and resid 590 through 594 removed outlier: 3.652A pdb=" N VAL A 604 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 634 through 637 Processing sheet with id=AB2, first strand: chain 'A' and resid 660 through 663 removed outlier: 4.139A pdb=" N GLY A 660 " --> pdb=" O ILE A 684 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 576 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: 1.99 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1823 1.34 - 1.46: 1140 1.46 - 1.58: 2556 1.58 - 1.69: 3 1.69 - 1.81: 40 Bond restraints: 5562 Sorted by residual: bond pdb=" C5 GDP A 701 " pdb=" C4 GDP A 701 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CA GLY A 170 " pdb=" C GLY A 170 " ideal model delta sigma weight residual 1.523 1.513 0.010 1.19e-02 7.06e+03 7.68e-01 bond pdb=" C PHE A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 7.16e-01 bond pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.68e-02 3.54e+03 6.30e-01 bond pdb=" CG1 ILE A 495 " pdb=" CD1 ILE A 495 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.18e-01 ... (remaining 5557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 7422 1.73 - 3.46: 114 3.46 - 5.18: 13 5.18 - 6.91: 6 6.91 - 8.64: 1 Bond angle restraints: 7556 Sorted by residual: angle pdb=" C ASN A 49 " pdb=" CA ASN A 49 " pdb=" CB ASN A 49 " ideal model delta sigma weight residual 110.42 116.86 -6.44 1.99e+00 2.53e-01 1.05e+01 angle pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 113.28 109.65 3.63 1.22e+00 6.72e-01 8.83e+00 angle pdb=" CB MET A 483 " pdb=" CG MET A 483 " pdb=" SD MET A 483 " ideal model delta sigma weight residual 112.70 121.34 -8.64 3.00e+00 1.11e-01 8.29e+00 angle pdb=" CB LYS A 674 " pdb=" CG LYS A 674 " pdb=" CD LYS A 674 " ideal model delta sigma weight residual 111.30 116.50 -5.20 2.30e+00 1.89e-01 5.11e+00 angle pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " pdb=" CG GLN A 234 " ideal model delta sigma weight residual 114.10 117.98 -3.88 2.00e+00 2.50e-01 3.77e+00 ... (remaining 7551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 2926 15.50 - 31.00: 314 31.00 - 46.50: 74 46.50 - 62.00: 11 62.00 - 77.50: 4 Dihedral angle restraints: 3329 sinusoidal: 1355 harmonic: 1974 Sorted by residual: dihedral pdb=" CA LEU A 507 " pdb=" C LEU A 507 " pdb=" N LEU A 508 " pdb=" CA LEU A 508 " ideal model delta harmonic sigma weight residual -180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 273 " pdb=" C LYS A 273 " pdb=" N TYR A 274 " pdb=" CA TYR A 274 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ALA A 474 " pdb=" C ALA A 474 " pdb=" N MET A 475 " pdb=" CA MET A 475 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 3326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 580 0.036 - 0.072: 167 0.072 - 0.108: 59 0.108 - 0.144: 24 0.144 - 0.180: 1 Chirality restraints: 831 Sorted by residual: chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 167 " pdb=" N ILE A 167 " pdb=" C ILE A 167 " pdb=" CB ILE A 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE A 589 " pdb=" N ILE A 589 " pdb=" C ILE A 589 " pdb=" CB ILE A 589 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 828 not shown) Planarity restraints: 984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 344 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 345 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 110 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 111 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 37 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 38 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.016 5.00e-02 4.00e+02 ... (remaining 981 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 766 2.76 - 3.29: 5088 3.29 - 3.83: 9027 3.83 - 4.36: 10792 4.36 - 4.90: 18801 Nonbonded interactions: 44474 Sorted by model distance: nonbonded pdb=" OE2 GLU A 606 " pdb=" NZ LYS A 649 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 250 " pdb=" OE1 GLU A 557 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A 365 " pdb=" OE2 GLU A 366 " model vdw 2.265 3.040 nonbonded pdb=" O PRO A 111 " pdb=" OH TYR A 115 " model vdw 2.278 3.040 nonbonded pdb=" NZ LYS A 364 " pdb=" O CYS A 370 " model vdw 2.315 3.120 ... (remaining 44469 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: 7.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.070 Find NCS groups from input model: 0.060 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 0.031 5562 Z= 0.163 Angle : 0.542 8.638 7556 Z= 0.279 Chirality : 0.043 0.180 831 Planarity : 0.003 0.060 984 Dihedral : 13.533 77.501 2061 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.34), residues: 682 helix: 1.57 (0.51), residues: 111 sheet: -0.65 (0.34), residues: 252 loop : -0.51 (0.37), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 241 HIS 0.003 0.001 HIS A 494 PHE 0.010 0.001 PHE A 39 TYR 0.011 0.001 TYR A 168 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.635 Fit side-chains REVERT: A 94 ASP cc_start: 0.8283 (t0) cc_final: 0.8044 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2041 time to fit residues: 10.1126 Evaluate side-chains 26 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5562 Z= 0.258 Angle : 0.554 9.973 7556 Z= 0.279 Chirality : 0.044 0.158 831 Planarity : 0.003 0.038 984 Dihedral : 4.586 26.653 756 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.34), residues: 682 helix: 1.35 (0.50), residues: 120 sheet: -0.76 (0.33), residues: 253 loop : -0.33 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.002 0.001 HIS A 134 PHE 0.013 0.001 PHE A 59 TYR 0.019 0.001 TYR A 551 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.697 Fit side-chains REVERT: A 94 ASP cc_start: 0.8244 (t0) cc_final: 0.7897 (t0) REVERT: A 400 ASP cc_start: 0.8399 (t0) cc_final: 0.8191 (t0) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1858 time to fit residues: 9.4451 Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5562 Z= 0.251 Angle : 0.531 7.810 7556 Z= 0.267 Chirality : 0.043 0.151 831 Planarity : 0.003 0.033 984 Dihedral : 4.601 27.374 756 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.50 % Allowed : 7.23 % Favored : 92.27 % 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: -0.42 (0.34), residues: 682 helix: 1.41 (0.49), residues: 119 sheet: -0.74 (0.33), residues: 255 loop : -0.39 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.001 0.000 HIS A 461 PHE 0.010 0.001 PHE A 392 TYR 0.017 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8273 (t0) cc_final: 0.7908 (t0) REVERT: A 227 MET cc_start: 0.9112 (mmm) cc_final: 0.8636 (tpt) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1992 time to fit residues: 9.1465 Evaluate side-chains 32 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5562 Z= 0.252 Angle : 0.524 6.443 7556 Z= 0.265 Chirality : 0.043 0.163 831 Planarity : 0.003 0.034 984 Dihedral : 4.621 27.880 756 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.18 % Allowed : 9.08 % Favored : 89.75 % 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: -0.44 (0.34), residues: 682 helix: 1.46 (0.49), residues: 119 sheet: -0.79 (0.33), residues: 255 loop : -0.40 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.002 0.001 HIS A 494 PHE 0.012 0.001 PHE A 59 TYR 0.016 0.001 TYR A 551 ARG 0.002 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8314 (t0) cc_final: 0.7931 (t0) REVERT: A 227 MET cc_start: 0.9136 (mmm) cc_final: 0.8624 (tpt) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.1970 time to fit residues: 10.2967 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.0770 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5562 Z= 0.185 Angle : 0.512 8.400 7556 Z= 0.254 Chirality : 0.043 0.181 831 Planarity : 0.003 0.033 984 Dihedral : 4.504 28.164 756 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 9.41 % Favored : 89.58 % 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: -0.32 (0.34), residues: 682 helix: 1.48 (0.49), residues: 120 sheet: -0.71 (0.34), residues: 249 loop : -0.31 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.002 0.000 HIS A 494 PHE 0.011 0.001 PHE A 59 TYR 0.016 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8313 (t0) cc_final: 0.7923 (t0) REVERT: A 227 MET cc_start: 0.9134 (mmm) cc_final: 0.8591 (tpt) outliers start: 6 outliers final: 4 residues processed: 38 average time/residue: 0.1747 time to fit residues: 9.4694 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5562 Z= 0.218 Angle : 0.515 7.968 7556 Z= 0.257 Chirality : 0.043 0.160 831 Planarity : 0.003 0.035 984 Dihedral : 4.548 27.633 756 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.67 % Allowed : 10.92 % Favored : 88.40 % 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: -0.35 (0.34), residues: 682 helix: 1.53 (0.49), residues: 119 sheet: -0.74 (0.33), residues: 255 loop : -0.32 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 278 HIS 0.002 0.001 HIS A 494 PHE 0.011 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.692 Fit side-chains REVERT: A 94 ASP cc_start: 0.8335 (t0) cc_final: 0.7938 (t0) REVERT: A 227 MET cc_start: 0.9135 (mmm) cc_final: 0.8575 (tpt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1923 time to fit residues: 9.5410 Evaluate side-chains 34 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5562 Z= 0.176 Angle : 0.512 7.706 7556 Z= 0.253 Chirality : 0.042 0.159 831 Planarity : 0.003 0.038 984 Dihedral : 4.450 30.033 756 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.18 % Allowed : 11.09 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.34), residues: 682 helix: 1.53 (0.49), residues: 120 sheet: -0.68 (0.33), residues: 255 loop : -0.27 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 278 HIS 0.002 0.000 HIS A 494 PHE 0.011 0.001 PHE A 59 TYR 0.016 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.738 Fit side-chains REVERT: A 94 ASP cc_start: 0.8341 (t0) cc_final: 0.7937 (t0) REVERT: A 227 MET cc_start: 0.9141 (mmm) cc_final: 0.8608 (tpt) outliers start: 7 outliers final: 4 residues processed: 38 average time/residue: 0.1830 time to fit residues: 9.9783 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 chunk 6 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5562 Z= 0.254 Angle : 0.546 8.126 7556 Z= 0.269 Chirality : 0.043 0.203 831 Planarity : 0.003 0.037 984 Dihedral : 4.643 28.058 756 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 11.93 % Favored : 87.06 % 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: -0.31 (0.34), residues: 682 helix: 1.54 (0.49), residues: 119 sheet: -0.70 (0.33), residues: 255 loop : -0.31 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 278 HIS 0.002 0.001 HIS A 494 PHE 0.011 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.678 Fit side-chains REVERT: A 94 ASP cc_start: 0.8368 (t0) cc_final: 0.7949 (t0) REVERT: A 227 MET cc_start: 0.9135 (mmm) cc_final: 0.8573 (tpt) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.1945 time to fit residues: 9.9574 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5562 Z= 0.228 Angle : 0.547 8.244 7556 Z= 0.268 Chirality : 0.043 0.182 831 Planarity : 0.003 0.040 984 Dihedral : 4.625 29.743 756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.23 % 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: -0.29 (0.34), residues: 682 helix: 1.54 (0.49), residues: 119 sheet: -0.67 (0.33), residues: 255 loop : -0.31 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS A 494 PHE 0.012 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.724 Fit side-chains REVERT: A 94 ASP cc_start: 0.8377 (t0) cc_final: 0.8027 (t0) REVERT: A 227 MET cc_start: 0.9132 (mmm) cc_final: 0.8578 (tpt) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1734 time to fit residues: 9.1069 Evaluate side-chains 36 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5562 Z= 0.234 Angle : 0.547 8.694 7556 Z= 0.268 Chirality : 0.043 0.168 831 Planarity : 0.003 0.040 984 Dihedral : 4.642 29.840 756 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.67 % Allowed : 12.27 % Favored : 87.06 % 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: -0.30 (0.34), residues: 682 helix: 1.55 (0.49), residues: 119 sheet: -0.69 (0.33), residues: 255 loop : -0.29 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 337 HIS 0.002 0.001 HIS A 494 PHE 0.012 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.003 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.709 Fit side-chains REVERT: A 94 ASP cc_start: 0.8384 (t0) cc_final: 0.8028 (t0) REVERT: A 227 MET cc_start: 0.9136 (mmm) cc_final: 0.8581 (tpt) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1845 time to fit residues: 8.9095 Evaluate side-chains 35 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073508 restraints weight = 11256.976| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.33 r_work: 0.3029 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5562 Z= 0.204 Angle : 0.533 8.664 7556 Z= 0.261 Chirality : 0.043 0.167 831 Planarity : 0.003 0.040 984 Dihedral : 4.567 31.249 756 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.84 % Allowed : 12.10 % Favored : 87.06 % 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: -0.25 (0.34), residues: 682 helix: 1.51 (0.49), residues: 120 sheet: -0.65 (0.33), residues: 255 loop : -0.25 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 337 HIS 0.002 0.000 HIS A 494 PHE 0.011 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.004 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2114.77 seconds wall clock time: 38 minutes 53.89 seconds (2333.89 seconds total)