Starting phenix.real_space_refine on Thu Mar 6 08:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_41574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_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/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_41574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_41574.map" model { file = "/net/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_41574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tr9_41574/03_2025/8tr9_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.65, per 1000 atoms: 1.04 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: 1.19 Conformation dependent library (CDL) restraints added in 608.7 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: 0.64 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: 1.92 Time building geometry restraints manager: 1.43 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: 7.770 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.050 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- 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 : 0.653 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: 0.1980 time to fit residues: 9.7917 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 : 0.636 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.091416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073294 restraints weight = 11157.341| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.36 r_work: 0.3019 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 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 : 0.596 Fit side-chains REVERT: A 94 ASP cc_start: 0.8514 (t0) cc_final: 0.8111 (t0) REVERT: A 400 ASP cc_start: 0.8778 (t0) cc_final: 0.8550 (t0) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1750 time to fit residues: 8.8654 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 : 0.581 ------------------------------------------------------------------------------- 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 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073663 restraints weight = 11271.648| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.37 r_work: 0.3042 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1078 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= 0.199 Angle : 0.513 8.042 7556 Z= 0.258 Chirality : 0.043 0.148 831 Planarity : 0.003 0.034 984 Dihedral : 4.491 26.558 756 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.50 % Allowed : 7.06 % 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: -0.34 (0.34), residues: 682 helix: 1.39 (0.49), residues: 120 sheet: -0.69 (0.34), residues: 249 loop : -0.32 (0.37), residues: 313 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 39 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 : 0.654 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8542 (t0) cc_final: 0.8093 (t0) REVERT: A 227 MET cc_start: 0.9400 (mmm) cc_final: 0.8967 (tpt) REVERT: A 400 ASP cc_start: 0.8764 (t0) cc_final: 0.8529 (t0) outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.1778 time to fit residues: 8.3712 Evaluate side-chains 30 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073464 restraints weight = 11514.628| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.39 r_work: 0.3019 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5562 Z= 0.206 Angle : 0.502 6.540 7556 Z= 0.254 Chirality : 0.043 0.163 831 Planarity : 0.003 0.034 984 Dihedral : 4.505 26.634 756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.01 % Allowed : 9.08 % Favored : 89.92 % 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: 1.42 (0.49), residues: 120 sheet: -0.71 (0.34), residues: 249 loop : -0.32 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 241 HIS 0.002 0.001 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 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 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8544 (t0) cc_final: 0.8092 (t0) REVERT: A 227 MET cc_start: 0.9410 (mmm) cc_final: 0.8941 (tpt) outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.1760 time to fit residues: 8.9338 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 : 0.664 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 7 optimal weight: 0.0050 chunk 2 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 overall best weight: 0.0708 ------------------------------------------------------------------------------- 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** A 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.104478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082331 restraints weight = 11479.338| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.38 r_work: 0.3131 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5562 Z= 0.125 Angle : 0.487 8.293 7556 Z= 0.242 Chirality : 0.042 0.163 831 Planarity : 0.003 0.035 984 Dihedral : 4.232 28.724 756 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.84 % Allowed : 8.57 % Favored : 90.59 % 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: -0.19 (0.34), residues: 682 helix: 1.55 (0.49), residues: 120 sheet: -0.50 (0.35), residues: 240 loop : -0.34 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.002 0.000 HIS A 494 PHE 0.009 0.001 PHE A 59 TYR 0.017 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 47 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8518 (t0) cc_final: 0.8047 (t0) REVERT: A 227 MET cc_start: 0.9362 (mmm) cc_final: 0.8918 (tpt) REVERT: A 640 ASP cc_start: 0.8714 (t0) cc_final: 0.8380 (p0) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1542 time to fit residues: 10.2183 Evaluate side-chains 39 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.0000 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074823 restraints weight = 11219.197| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.28 r_work: 0.3057 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5562 Z= 0.194 Angle : 0.495 7.461 7556 Z= 0.246 Chirality : 0.043 0.178 831 Planarity : 0.003 0.034 984 Dihedral : 4.348 26.159 756 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.34 % Allowed : 9.58 % Favored : 89.08 % 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: -0.17 (0.34), residues: 682 helix: 1.53 (0.49), residues: 120 sheet: -0.57 (0.33), residues: 255 loop : -0.21 (0.38), residues: 307 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 0.010 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 44 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 94 ASP cc_start: 0.8498 (t0) cc_final: 0.8042 (t0) REVERT: A 640 ASP cc_start: 0.8682 (t0) cc_final: 0.8451 (p0) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1631 time to fit residues: 9.9655 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 : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075003 restraints weight = 11283.956| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.36 r_work: 0.3059 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1542 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= 0.181 Angle : 0.515 7.824 7556 Z= 0.254 Chirality : 0.042 0.159 831 Planarity : 0.003 0.034 984 Dihedral : 4.387 27.838 756 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 : 0.84 % Allowed : 10.76 % 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: -0.16 (0.34), residues: 682 helix: 1.57 (0.49), residues: 120 sheet: -0.56 (0.33), residues: 255 loop : -0.22 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 278 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 0.003 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 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.624 Fit side-chains REVERT: A 41 LEU cc_start: 0.8558 (tt) cc_final: 0.8290 (tt) REVERT: A 94 ASP cc_start: 0.8533 (t0) cc_final: 0.8065 (t0) REVERT: A 130 PHE cc_start: 0.8622 (m-10) cc_final: 0.8318 (m-10) REVERT: A 227 MET cc_start: 0.9336 (mmm) cc_final: 0.8812 (tpt) outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.1740 time to fit residues: 9.1472 Evaluate side-chains 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 46 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074386 restraints weight = 11333.329| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.37 r_work: 0.3051 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5562 Z= 0.186 Angle : 0.512 7.702 7556 Z= 0.252 Chirality : 0.042 0.155 831 Planarity : 0.003 0.038 984 Dihedral : 4.411 27.623 756 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.18 % Allowed : 11.26 % Favored : 87.56 % 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: -0.15 (0.34), residues: 682 helix: 1.56 (0.49), residues: 120 sheet: -0.56 (0.33), residues: 255 loop : -0.20 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.004 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 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.629 Fit side-chains REVERT: A 41 LEU cc_start: 0.8561 (tt) cc_final: 0.8282 (tt) REVERT: A 94 ASP cc_start: 0.8549 (t0) cc_final: 0.8058 (t0) REVERT: A 130 PHE cc_start: 0.8628 (m-10) cc_final: 0.8352 (m-10) REVERT: A 227 MET cc_start: 0.9343 (mmm) cc_final: 0.8733 (tpt) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 0.1689 time to fit residues: 9.3650 Evaluate side-chains 38 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 465 LEU 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 32 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 43 optimal weight: 0.0040 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.0470 overall best weight: 0.3870 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.102393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079589 restraints weight = 11467.024| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.41 r_work: 0.3087 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5562 Z= 0.162 Angle : 0.513 8.208 7556 Z= 0.251 Chirality : 0.042 0.151 831 Planarity : 0.003 0.037 984 Dihedral : 4.349 28.781 756 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.84 % Allowed : 11.93 % 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: -0.09 (0.34), residues: 682 helix: 1.59 (0.49), residues: 120 sheet: -0.44 (0.34), residues: 250 loop : -0.24 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 278 HIS 0.002 0.000 HIS A 494 PHE 0.010 0.001 PHE A 59 TYR 0.015 0.001 TYR A 551 ARG 0.004 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 40 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.667 Fit side-chains REVERT: A 41 LEU cc_start: 0.8533 (tt) cc_final: 0.8246 (tt) REVERT: A 94 ASP cc_start: 0.8579 (t0) cc_final: 0.8176 (t0) REVERT: A 227 MET cc_start: 0.9335 (mmm) cc_final: 0.8682 (tpt) REVERT: A 640 ASP cc_start: 0.8719 (t70) cc_final: 0.8479 (p0) outliers start: 5 outliers final: 5 residues processed: 39 average time/residue: 0.1703 time to fit residues: 9.5278 Evaluate side-chains 39 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 465 LEU 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 25 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072941 restraints weight = 11390.793| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.35 r_work: 0.3017 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5562 Z= 0.237 Angle : 0.538 8.453 7556 Z= 0.264 Chirality : 0.043 0.157 831 Planarity : 0.003 0.036 984 Dihedral : 4.549 27.253 756 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: -0.16 (0.34), residues: 682 helix: 1.58 (0.49), residues: 119 sheet: -0.50 (0.33), residues: 250 loop : -0.28 (0.38), residues: 313 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 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 37 residues out of total 595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.591 Fit side-chains REVERT: A 94 ASP cc_start: 0.8597 (t0) cc_final: 0.8201 (t0) REVERT: A 227 MET cc_start: 0.9342 (mmm) cc_final: 0.8713 (tpt) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.1729 time to fit residues: 8.7996 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 : 0.551 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.092150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074127 restraints weight = 11380.108| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.36 r_work: 0.3045 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1615 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= 0.199 Angle : 0.548 8.517 7556 Z= 0.264 Chirality : 0.043 0.154 831 Planarity : 0.003 0.040 984 Dihedral : 4.485 29.474 756 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.84 % Allowed : 11.93 % 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: -0.13 (0.34), residues: 682 helix: 1.55 (0.49), residues: 120 sheet: -0.47 (0.34), residues: 250 loop : -0.26 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 278 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: 3332.38 seconds wall clock time: 57 minutes 53.29 seconds (3473.29 seconds total)