Starting phenix.real_space_refine on Tue Feb 11 03:26:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh6_14725/02_2025/7zh6_14725_neut.cif" } resolution = 3.67 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2501 2.51 5 N 621 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3771 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3746 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain breaks: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'C0R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.86 Number of scatterers: 3771 At special positions: 0 Unit cell: (101.64, 63.36, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 627 8.00 N 621 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 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: 1.01 Conformation dependent library (CDL) restraints added in 455.2 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 79.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.691A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 43 removed outlier: 4.419A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.789A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.941A pdb=" N GLU A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 179 removed outlier: 3.677A pdb=" N LEU A 154 " --> pdb=" O ASN A 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.722A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.531A pdb=" N PHE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 263 Proline residue: A 258 - end of helix removed outlier: 3.506A pdb=" N TYR A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Proline residue: A 277 - end of helix removed outlier: 3.644A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 344 through 372 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.749A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.557A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 removed outlier: 3.921A pdb=" N PHE A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 461 removed outlier: 4.363A pdb=" N ARG A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.561A pdb=" N VAL A 470 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 3.946A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.982A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.659A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 532 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 3.715A pdb=" N TRP A 50 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 257 hydrogen bonds defined for protein. 759 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: 1.02 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 621 1.33 - 1.45: 1028 1.45 - 1.57: 2188 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3867 Sorted by residual: bond pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.00e-02 1.00e+04 9.98e+00 bond pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.62e+00 bond pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE A 264 " pdb=" CA ILE A 264 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.83e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 4985 1.95 - 3.89: 251 3.89 - 5.84: 23 5.84 - 7.78: 7 7.78 - 9.73: 3 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 114.62 108.91 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 114.92 108.98 5.94 1.19e+00 7.06e-01 2.50e+01 angle pdb=" O GLU A 533 " pdb=" C GLU A 533 " pdb=" N LYS A 534 " ideal model delta sigma weight residual 122.03 126.35 -4.32 1.08e+00 8.57e-01 1.60e+01 angle pdb=" C GLU A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.71 107.31 4.40 1.15e+00 7.56e-01 1.46e+01 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 2011 18.07 - 36.14: 212 36.14 - 54.21: 47 54.21 - 72.28: 9 72.28 - 90.35: 7 Dihedral angle restraints: 2286 sinusoidal: 929 harmonic: 1357 Sorted by residual: dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -155.72 69.72 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" C ARG A 298 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" CB ARG A 298 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CB GLU A 519 " pdb=" CG GLU A 519 " pdb=" CD GLU A 519 " pdb=" OE1 GLU A 519 " ideal model delta sinusoidal sigma weight residual 0.00 -90.35 90.35 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 429 0.046 - 0.092: 108 0.092 - 0.138: 57 0.138 - 0.184: 17 0.184 - 0.230: 6 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 186 " pdb=" N LEU A 186 " pdb=" C LEU A 186 " pdb=" CB LEU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 614 not shown) Planarity restraints: 647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 C0R A 601 " -0.017 2.00e-02 2.50e+03 8.14e-02 8.29e+01 pdb=" C3 C0R A 601 " 0.100 2.00e-02 2.50e+03 pdb=" C4 C0R A 601 " -0.129 2.00e-02 2.50e+03 pdb=" C5 C0R A 601 " -0.027 2.00e-02 2.50e+03 pdb=" C6 C0R A 601 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL A 183 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 183 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 184 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 262 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C TYR A 262 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 262 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 263 " 0.014 2.00e-02 2.50e+03 ... (remaining 644 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 8 2.27 - 2.92: 1669 2.92 - 3.58: 6083 3.58 - 4.24: 8096 4.24 - 4.90: 13806 Nonbonded interactions: 29662 Sorted by model distance: nonbonded pdb=" CD1 ILE A 523 " pdb=" OE1 GLU A 533 " model vdw 1.607 3.460 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.143 3.040 nonbonded pdb=" CE2 PHE A 4 " pdb=" NE ARG A 293 " model vdw 2.154 3.420 nonbonded pdb=" O PHE A 468 " pdb=" OG SER A 471 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.235 3.120 ... (remaining 29657 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.006 0.062 3867 Z= 0.386 Angle : 0.900 9.731 5269 Z= 0.586 Chirality : 0.057 0.230 617 Planarity : 0.005 0.081 647 Dihedral : 15.908 90.348 1410 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.26 % Allowed : 28.46 % Favored : 70.28 % 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: 0.99 (0.40), residues: 468 helix: 1.81 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.22 (0.46), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.016 0.001 PHE A 41 TYR 0.008 0.001 TYR A 174 ARG 0.002 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.388 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.1259 time to fit residues: 16.8309 Evaluate side-chains 89 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 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 9 GLN A 150 ASN A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148641 restraints weight = 6960.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.153298 restraints weight = 3679.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156419 restraints weight = 2303.180| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3867 Z= 0.237 Angle : 0.676 9.000 5269 Z= 0.333 Chirality : 0.042 0.160 617 Planarity : 0.005 0.049 647 Dihedral : 4.448 33.439 579 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.04 % Allowed : 24.94 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.39), residues: 468 helix: 1.90 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -3.18 (0.48), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 137 PHE 0.014 0.002 PHE A 213 TYR 0.010 0.001 TYR A 174 ARG 0.004 0.001 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.447 Fit side-chains REVERT: A 14 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6737 (m-80) REVERT: A 124 LEU cc_start: 0.8231 (tt) cc_final: 0.7870 (mp) REVERT: A 290 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6170 (mt-10) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.1187 time to fit residues: 17.5039 Evaluate side-chains 103 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 494 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 457 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 = 0.4123 r_free = 0.4123 target = 0.166910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145695 restraints weight = 6727.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150268 restraints weight = 3490.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153350 restraints weight = 2152.578| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3867 Z= 0.246 Angle : 0.661 8.429 5269 Z= 0.326 Chirality : 0.041 0.155 617 Planarity : 0.004 0.039 647 Dihedral : 4.366 31.654 579 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.79 % Allowed : 25.19 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.39), residues: 468 helix: 1.92 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -3.02 (0.50), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 PHE 0.015 0.002 PHE A 213 TYR 0.015 0.002 TYR A 284 ARG 0.003 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.380 Fit side-chains REVERT: A 14 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: A 124 LEU cc_start: 0.8321 (tt) cc_final: 0.7975 (mp) REVERT: A 290 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6307 (mt-10) outliers start: 23 outliers final: 18 residues processed: 114 average time/residue: 0.1085 time to fit residues: 16.4162 Evaluate side-chains 112 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.166641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144896 restraints weight = 6797.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.149442 restraints weight = 3661.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.152606 restraints weight = 2296.043| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3867 Z= 0.209 Angle : 0.609 8.908 5269 Z= 0.304 Chirality : 0.039 0.158 617 Planarity : 0.004 0.036 647 Dihedral : 4.366 34.473 579 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.54 % Allowed : 27.20 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 468 helix: 2.01 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.97 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 PHE 0.014 0.001 PHE A 213 TYR 0.011 0.001 TYR A 461 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.384 Fit side-chains REVERT: A 14 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 93 TYR cc_start: 0.6224 (m-80) cc_final: 0.5601 (m-80) REVERT: A 124 LEU cc_start: 0.8389 (tt) cc_final: 0.7917 (mp) outliers start: 22 outliers final: 20 residues processed: 111 average time/residue: 0.1147 time to fit residues: 16.7232 Evaluate side-chains 109 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 25 optimal weight: 0.0970 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145599 restraints weight = 6998.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150249 restraints weight = 3747.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.153570 restraints weight = 2348.300| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3867 Z= 0.208 Angle : 0.622 9.210 5269 Z= 0.303 Chirality : 0.039 0.159 617 Planarity : 0.004 0.037 647 Dihedral : 4.303 34.844 579 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.05 % Allowed : 28.21 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 468 helix: 2.00 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.96 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 213 TYR 0.011 0.001 TYR A 461 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.374 Fit side-chains REVERT: A 93 TYR cc_start: 0.6131 (m-80) cc_final: 0.5370 (m-80) REVERT: A 124 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 282 LEU cc_start: 0.8588 (tp) cc_final: 0.8383 (tp) outliers start: 24 outliers final: 18 residues processed: 107 average time/residue: 0.1135 time to fit residues: 16.0261 Evaluate side-chains 104 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 3 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.170091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148970 restraints weight = 6714.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153659 restraints weight = 3555.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156887 restraints weight = 2195.328| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3867 Z= 0.197 Angle : 0.603 9.379 5269 Z= 0.296 Chirality : 0.039 0.167 617 Planarity : 0.004 0.039 647 Dihedral : 4.164 32.970 579 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.04 % Allowed : 29.22 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.39), residues: 468 helix: 1.98 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.88 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 48 PHE 0.013 0.001 PHE A 213 TYR 0.010 0.001 TYR A 461 ARG 0.001 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.316 Fit side-chains REVERT: A 93 TYR cc_start: 0.6086 (m-80) cc_final: 0.5403 (m-80) REVERT: A 124 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7633 (mp) outliers start: 20 outliers final: 14 residues processed: 105 average time/residue: 0.1132 time to fit residues: 16.0167 Evaluate side-chains 97 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145357 restraints weight = 6738.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150032 restraints weight = 3529.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153289 restraints weight = 2170.485| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3867 Z= 0.252 Angle : 0.654 9.407 5269 Z= 0.322 Chirality : 0.041 0.239 617 Planarity : 0.004 0.040 647 Dihedral : 4.328 33.411 579 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.05 % Allowed : 28.21 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.39), residues: 468 helix: 1.91 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.97 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 131 HIS 0.002 0.001 HIS A 48 PHE 0.015 0.002 PHE A 41 TYR 0.011 0.002 TYR A 93 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.410 Fit side-chains REVERT: A 124 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7528 (mp) outliers start: 24 outliers final: 21 residues processed: 108 average time/residue: 0.1199 time to fit residues: 17.2018 Evaluate side-chains 110 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 162 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.165270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143966 restraints weight = 7046.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.148603 restraints weight = 3737.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.151787 restraints weight = 2327.555| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3867 Z= 0.228 Angle : 0.664 9.689 5269 Z= 0.323 Chirality : 0.041 0.214 617 Planarity : 0.004 0.043 647 Dihedral : 4.277 33.548 579 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.79 % Allowed : 29.97 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.39), residues: 468 helix: 1.90 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.94 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 PHE 0.014 0.001 PHE A 213 TYR 0.008 0.001 TYR A 461 ARG 0.008 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.418 Fit side-chains REVERT: A 34 PHE cc_start: 0.6823 (m-80) cc_final: 0.6522 (m-80) REVERT: A 124 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7491 (mp) REVERT: A 150 ASN cc_start: 0.7208 (m-40) cc_final: 0.6811 (m-40) REVERT: A 343 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.6892 (tpm170) outliers start: 19 outliers final: 16 residues processed: 107 average time/residue: 0.1198 time to fit residues: 16.8087 Evaluate side-chains 106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.164828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143739 restraints weight = 6889.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.148278 restraints weight = 3668.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.151425 restraints weight = 2295.900| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3867 Z= 0.243 Angle : 0.669 9.691 5269 Z= 0.330 Chirality : 0.041 0.207 617 Planarity : 0.004 0.043 647 Dihedral : 4.288 33.110 579 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.05 % Allowed : 29.22 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 468 helix: 1.88 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.90 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.001 0.001 HIS A 48 PHE 0.014 0.001 PHE A 213 TYR 0.007 0.001 TYR A 49 ARG 0.007 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.388 Fit side-chains REVERT: A 34 PHE cc_start: 0.6870 (m-80) cc_final: 0.6552 (m-80) REVERT: A 124 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7437 (mp) REVERT: A 237 LYS cc_start: 0.9039 (tppt) cc_final: 0.8787 (tppp) REVERT: A 527 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6908 (tp30) REVERT: A 530 ASP cc_start: 0.7763 (t0) cc_final: 0.7348 (t0) outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.1127 time to fit residues: 16.1245 Evaluate side-chains 110 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 457 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 = 0.4062 r_free = 0.4062 target = 0.163678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.142579 restraints weight = 7026.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147230 restraints weight = 3692.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150417 restraints weight = 2278.892| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3867 Z= 0.256 Angle : 0.692 10.562 5269 Z= 0.342 Chirality : 0.043 0.293 617 Planarity : 0.005 0.044 647 Dihedral : 4.370 33.072 579 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.04 % Allowed : 29.22 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.39), residues: 468 helix: 1.83 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.96 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.002 0.001 HIS A 48 PHE 0.015 0.001 PHE A 41 TYR 0.008 0.001 TYR A 49 ARG 0.007 0.000 ARG A 343 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.411 Fit side-chains REVERT: A 34 PHE cc_start: 0.7023 (m-80) cc_final: 0.6795 (m-80) REVERT: A 124 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7383 (mp) REVERT: A 527 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7023 (tp30) REVERT: A 530 ASP cc_start: 0.7841 (t0) cc_final: 0.7422 (t0) outliers start: 20 outliers final: 19 residues processed: 103 average time/residue: 0.1108 time to fit residues: 15.3315 Evaluate side-chains 108 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 37 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 457 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 = 0.4065 r_free = 0.4065 target = 0.164011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142951 restraints weight = 6979.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147518 restraints weight = 3695.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150644 restraints weight = 2304.562| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3867 Z= 0.250 Angle : 0.685 9.893 5269 Z= 0.341 Chirality : 0.042 0.290 617 Planarity : 0.005 0.045 647 Dihedral : 4.338 33.124 579 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.29 % Allowed : 29.97 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.39), residues: 468 helix: 1.86 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.96 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.001 HIS A 48 PHE 0.014 0.001 PHE A 41 TYR 0.008 0.001 TYR A 49 ARG 0.007 0.000 ARG A 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.56 seconds wall clock time: 27 minutes 8.65 seconds (1628.65 seconds total)