Starting phenix.real_space_refine on Thu Jul 18 21:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_14725_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_14725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_14725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_14725_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/07_2024/7zh6_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 Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.53, per 1000 atoms: 0.94 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 670.8 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: 0.37 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: 1.03 Time building geometry restraints manager: 1.81 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: 98.85 - 105.87: 93 105.87 - 112.90: 2048 112.90 - 119.92: 1382 119.92 - 126.95: 1694 126.95 - 133.97: 52 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 2.440 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 2.440 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.235 2.520 ... (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: 0.010 Normalize map: mean=0, sd=1: 1.920 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 16.330 Find NCS groups from input model: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- 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 fitting. 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: 0.1359 time to fit residues: 18.2658 Evaluate side-chains 89 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.9980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 18 GLN A 150 ASN A 414 ASN A 457 ASN A 467 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3867 Z= 0.255 Angle : 0.679 8.739 5269 Z= 0.335 Chirality : 0.042 0.161 617 Planarity : 0.005 0.052 647 Dihedral : 4.398 26.687 579 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.30 % Allowed : 24.94 % Favored : 68.77 % 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: 1.95 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -3.20 (0.49), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 358 HIS 0.001 0.001 HIS A 137 PHE 0.014 0.002 PHE A 213 TYR 0.011 0.002 TYR A 174 ARG 0.002 0.000 ARG A 310 *********************** 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 124 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.408 Fit side-chains REVERT: A 14 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: A 124 LEU cc_start: 0.8308 (tt) cc_final: 0.8035 (mp) REVERT: A 467 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.7967 (t0) outliers start: 25 outliers final: 17 residues processed: 113 average time/residue: 0.1171 time to fit residues: 17.6213 Evaluate side-chains 106 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 382 ASP 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 465 LEU Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1949 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= 0.219 Angle : 0.637 8.744 5269 Z= 0.311 Chirality : 0.040 0.160 617 Planarity : 0.004 0.040 647 Dihedral : 4.295 32.851 579 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.80 % Allowed : 25.19 % Favored : 68.01 % 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: 1.41 (0.39), residues: 468 helix: 2.02 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.96 (0.51), 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 137 PHE 0.015 0.001 PHE A 213 TYR 0.016 0.001 TYR A 284 ARG 0.002 0.000 ARG A 466 *********************** 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 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.424 Fit side-chains REVERT: A 14 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6748 (m-80) REVERT: A 124 LEU cc_start: 0.8343 (tt) cc_final: 0.7981 (mp) outliers start: 27 outliers final: 20 residues processed: 107 average time/residue: 0.1141 time to fit residues: 16.2221 Evaluate side-chains 108 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 382 ASP 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 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3867 Z= 0.298 Angle : 0.679 9.043 5269 Z= 0.341 Chirality : 0.042 0.154 617 Planarity : 0.005 0.038 647 Dihedral : 4.549 32.033 579 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.81 % Allowed : 25.94 % Favored : 66.25 % 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: 1.24 (0.40), residues: 468 helix: 1.93 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -3.14 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.001 0.001 HIS A 137 PHE 0.017 0.002 PHE A 34 TYR 0.012 0.002 TYR A 93 ARG 0.003 0.000 ARG A 309 *********************** 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 124 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 0.408 Fit side-chains REVERT: A 14 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 93 TYR cc_start: 0.6251 (m-80) cc_final: 0.5690 (m-80) REVERT: A 124 LEU cc_start: 0.8381 (tt) cc_final: 0.7929 (mp) REVERT: A 224 MET cc_start: 0.8170 (ttm) cc_final: 0.7856 (ttm) REVERT: A 248 MET cc_start: 0.9063 (mmm) cc_final: 0.8861 (mmm) REVERT: A 347 MET cc_start: 0.8286 (ttt) cc_final: 0.8025 (ttt) outliers start: 31 outliers final: 26 residues processed: 114 average time/residue: 0.1205 time to fit residues: 17.9771 Evaluate side-chains 114 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 44 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 177 ASP 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 266 ASN 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 382 ASP 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 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3867 Z= 0.225 Angle : 0.633 8.136 5269 Z= 0.311 Chirality : 0.040 0.164 617 Planarity : 0.004 0.038 647 Dihedral : 4.447 33.300 579 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.55 % Allowed : 28.97 % Favored : 64.48 % 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: 1.35 (0.40), residues: 468 helix: 2.02 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -3.13 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.000 0.000 HIS A 137 PHE 0.015 0.001 PHE A 213 TYR 0.008 0.001 TYR A 49 ARG 0.006 0.000 ARG A 343 *********************** 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 124 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.494 Fit side-chains REVERT: A 14 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: A 93 TYR cc_start: 0.6141 (m-80) cc_final: 0.5537 (m-80) REVERT: A 124 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7795 (mp) REVERT: A 248 MET cc_start: 0.8992 (mmm) cc_final: 0.8769 (mmt) REVERT: A 347 MET cc_start: 0.8277 (ttt) cc_final: 0.8003 (ttt) outliers start: 26 outliers final: 21 residues processed: 114 average time/residue: 0.1210 time to fit residues: 17.9293 Evaluate side-chains 113 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 124 LEU 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 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 382 ASP 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 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3867 Z= 0.214 Angle : 0.638 9.665 5269 Z= 0.309 Chirality : 0.040 0.159 617 Planarity : 0.004 0.039 647 Dihedral : 4.286 33.402 579 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 7.56 % Allowed : 29.22 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.40), residues: 468 helix: 2.01 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -2.99 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.000 0.000 HIS A 137 PHE 0.014 0.001 PHE A 41 TYR 0.008 0.001 TYR A 461 ARG 0.006 0.000 ARG A 343 *********************** 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 127 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.426 Fit side-chains REVERT: A 14 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 34 PHE cc_start: 0.6932 (m-80) cc_final: 0.6660 (m-80) REVERT: A 93 TYR cc_start: 0.6089 (m-80) cc_final: 0.5480 (m-80) REVERT: A 124 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7590 (mp) REVERT: A 128 ARG cc_start: 0.6435 (tpm170) cc_final: 0.6200 (tpm170) REVERT: A 238 GLN cc_start: 0.8196 (mp10) cc_final: 0.7416 (mp10) REVERT: A 347 MET cc_start: 0.8253 (ttt) cc_final: 0.7980 (ttt) REVERT: A 527 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7014 (tp30) outliers start: 30 outliers final: 26 residues processed: 115 average time/residue: 0.1286 time to fit residues: 18.9300 Evaluate side-chains 118 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3867 Z= 0.239 Angle : 0.652 9.445 5269 Z= 0.316 Chirality : 0.041 0.166 617 Planarity : 0.005 0.039 647 Dihedral : 4.354 32.851 579 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.56 % Allowed : 29.72 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.40), residues: 468 helix: 1.94 (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 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.016 0.002 PHE A 41 TYR 0.008 0.001 TYR A 93 ARG 0.007 0.000 ARG A 343 *********************** 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 130 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 0.417 Fit side-chains REVERT: A 14 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6767 (m-80) REVERT: A 93 TYR cc_start: 0.6146 (m-80) cc_final: 0.5618 (m-80) REVERT: A 124 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 128 ARG cc_start: 0.6525 (tpm170) cc_final: 0.6292 (tpm170) REVERT: A 238 GLN cc_start: 0.8211 (mp10) cc_final: 0.7406 (mp10) REVERT: A 290 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: A 347 MET cc_start: 0.8257 (ttt) cc_final: 0.7991 (ttt) REVERT: A 527 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7127 (tp30) REVERT: A 530 ASP cc_start: 0.7687 (t0) cc_final: 0.7255 (t0) outliers start: 30 outliers final: 25 residues processed: 118 average time/residue: 0.1224 time to fit residues: 18.6040 Evaluate side-chains 123 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 266 ASN 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 302 ASP 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 382 ASP 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2880 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= 0.225 Angle : 0.650 9.580 5269 Z= 0.314 Chirality : 0.040 0.158 617 Planarity : 0.005 0.041 647 Dihedral : 4.299 33.426 579 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 7.81 % Allowed : 29.72 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.39), residues: 468 helix: 1.94 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.92 (0.53), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.015 0.001 PHE A 41 TYR 0.008 0.001 TYR A 49 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 129 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 0.414 Fit side-chains REVERT: A 14 PHE cc_start: 0.7098 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: A 34 PHE cc_start: 0.6990 (m-80) cc_final: 0.6764 (m-80) REVERT: A 93 TYR cc_start: 0.6199 (m-80) cc_final: 0.5679 (m-80) REVERT: A 124 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 237 LYS cc_start: 0.9066 (tppt) cc_final: 0.8729 (tppt) REVERT: A 238 GLN cc_start: 0.8135 (mp10) cc_final: 0.7855 (mp10) REVERT: A 290 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6368 (mt-10) REVERT: A 347 MET cc_start: 0.8256 (ttt) cc_final: 0.7970 (ttt) REVERT: A 527 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7079 (tp30) REVERT: A 530 ASP cc_start: 0.7687 (t0) cc_final: 0.7247 (t0) outliers start: 31 outliers final: 26 residues processed: 117 average time/residue: 0.1230 time to fit residues: 18.5595 Evaluate side-chains 121 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 266 ASN 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 302 ASP 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 382 ASP 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 440 THR 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3867 Z= 0.225 Angle : 0.644 9.690 5269 Z= 0.313 Chirality : 0.041 0.177 617 Planarity : 0.005 0.043 647 Dihedral : 4.284 33.200 579 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 8.06 % Allowed : 28.72 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.39), residues: 468 helix: 1.93 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -2.85 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.015 0.001 PHE A 41 TYR 0.008 0.001 TYR A 49 ARG 0.008 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 126 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 0.408 Fit side-chains REVERT: A 14 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: A 34 PHE cc_start: 0.6961 (m-80) cc_final: 0.6733 (m-80) REVERT: A 93 TYR cc_start: 0.6226 (m-80) cc_final: 0.5702 (m-80) REVERT: A 124 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 237 LYS cc_start: 0.9038 (tppt) cc_final: 0.8772 (tppt) REVERT: A 238 GLN cc_start: 0.8231 (mp10) cc_final: 0.7883 (mp10) REVERT: A 290 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: A 347 MET cc_start: 0.8248 (ttt) cc_final: 0.7960 (ttt) REVERT: A 527 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7099 (tp30) REVERT: A 530 ASP cc_start: 0.7689 (t0) cc_final: 0.7249 (t0) outliers start: 32 outliers final: 27 residues processed: 114 average time/residue: 0.1165 time to fit residues: 17.6403 Evaluate side-chains 121 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP 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 382 ASP 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 440 THR 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3867 Z= 0.252 Angle : 0.673 9.793 5269 Z= 0.328 Chirality : 0.041 0.150 617 Planarity : 0.005 0.041 647 Dihedral : 4.366 32.919 579 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 7.56 % Allowed : 29.72 % Favored : 62.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.40), residues: 468 helix: 1.93 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.93 (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 137 PHE 0.017 0.002 PHE A 41 TYR 0.009 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 122 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.433 Fit side-chains REVERT: A 14 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 34 PHE cc_start: 0.7195 (m-80) cc_final: 0.6963 (m-80) REVERT: A 93 TYR cc_start: 0.6247 (m-80) cc_final: 0.5718 (m-80) REVERT: A 124 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 237 LYS cc_start: 0.9091 (tppt) cc_final: 0.8817 (tppt) REVERT: A 238 GLN cc_start: 0.8183 (mp10) cc_final: 0.7911 (mp10) REVERT: A 290 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6353 (mt-10) REVERT: A 347 MET cc_start: 0.8235 (ttt) cc_final: 0.7961 (ttt) REVERT: A 527 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7110 (tp30) REVERT: A 530 ASP cc_start: 0.7725 (t0) cc_final: 0.7284 (t0) outliers start: 30 outliers final: 26 residues processed: 111 average time/residue: 0.1100 time to fit residues: 16.3344 Evaluate side-chains 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 177 ASP 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 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP 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 382 ASP 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 Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 0.0000 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 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 = 0.4035 r_free = 0.4035 target = 0.160690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140040 restraints weight = 6987.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144590 restraints weight = 3788.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147599 restraints weight = 2378.021| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3867 Z= 0.237 Angle : 0.677 11.086 5269 Z= 0.326 Chirality : 0.041 0.174 617 Planarity : 0.005 0.041 647 Dihedral : 4.344 33.214 579 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.30 % Allowed : 29.72 % Favored : 62.97 % 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: 1.33 (0.40), residues: 468 helix: 1.94 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -2.94 (0.52), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.016 0.002 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: 1238.33 seconds wall clock time: 22 minutes 45.92 seconds (1365.92 seconds total)