Starting phenix.real_space_refine on Thu Jul 18 21:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr8_14886/07_2024/7zr8_14886.cif" } resolution = 3.7 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= 0.012 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 18 5.16 5 C 2346 2.51 5 N 623 2.21 5 O 706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3693 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 13, 'TRANS': 231} Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 900 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.31, per 1000 atoms: 0.90 Number of scatterers: 3693 At special positions: 0 Unit cell: (68.06, 75.53, 111.22, 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 18 16.00 O 706 8.00 N 623 7.00 C 2346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 340 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 694.5 milliseconds 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 866 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 9.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.601A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.017A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.371A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.137A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.714A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 removed outlier: 7.131A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.569A pdb=" N LYS A 353 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.794A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.926A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY H 100 " --> pdb=" O PHE H 105 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE H 105 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.530A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.339A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 252 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: 0.99 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1178 1.34 - 1.46: 930 1.46 - 1.58: 1653 1.58 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 3784 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" C2 NAG A1301 " pdb=" N2 NAG A1301 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.08e-01 bond pdb=" C4 NAG A1301 " pdb=" O4 NAG A1301 " ideal model delta sigma weight residual 1.409 1.423 -0.014 2.00e-02 2.50e+03 4.82e-01 ... (remaining 3779 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 106 107.02 - 113.77: 2016 113.77 - 120.51: 1398 120.51 - 127.26: 1583 127.26 - 134.01: 34 Bond angle restraints: 5137 Sorted by residual: angle pdb=" N ILE L 29 " pdb=" CA ILE L 29 " pdb=" C ILE L 29 " ideal model delta sigma weight residual 111.77 109.00 2.77 1.04e+00 9.25e-01 7.10e+00 angle pdb=" C ALA A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 121.65 119.16 2.49 1.01e+00 9.80e-01 6.07e+00 angle pdb=" N ASP H 103 " pdb=" CA ASP H 103 " pdb=" CB ASP H 103 " ideal model delta sigma weight residual 113.65 110.44 3.21 1.47e+00 4.63e-01 4.78e+00 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 112.97 110.97 2.00 1.06e+00 8.90e-01 3.57e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 125.02 -3.48 1.91e+00 2.74e-01 3.32e+00 ... (remaining 5132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.18: 2044 10.18 - 20.36: 146 20.36 - 30.54: 47 30.54 - 40.72: 13 40.72 - 50.90: 5 Dihedral angle restraints: 2255 sinusoidal: 893 harmonic: 1362 Sorted by residual: dihedral pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " pdb=" CD1 LEU L 33 " ideal model delta sinusoidal sigma weight residual 180.00 129.10 50.90 3 1.50e+01 4.44e-03 8.95e+00 dihedral pdb=" CA PRO A 524 " pdb=" C PRO A 524 " pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" N TYR A 498 " pdb=" CA TYR A 498 " pdb=" CB TYR A 498 " pdb=" CG TYR A 498 " ideal model delta sinusoidal sigma weight residual -60.00 -108.10 48.10 3 1.50e+01 4.44e-03 8.59e+00 ... (remaining 2252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 340 0.030 - 0.059: 142 0.059 - 0.089: 30 0.089 - 0.118: 42 0.118 - 0.148: 4 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 399 " pdb=" N ILE A 399 " pdb=" C ILE A 399 " pdb=" CB ILE A 399 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 555 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO L 96 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 326 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 327 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 557 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 558 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 558 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 558 " -0.014 5.00e-02 4.00e+02 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 174 2.73 - 3.27: 3512 3.27 - 3.81: 5835 3.81 - 4.36: 7174 4.36 - 4.90: 12818 Nonbonded interactions: 29513 Sorted by model distance: nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.181 2.440 nonbonded pdb=" OG1 THR H 33 " pdb=" OG SER H 99 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.255 2.440 nonbonded pdb=" O LYS H 13 " pdb=" OG SER H 16 " model vdw 2.281 2.440 nonbonded pdb=" O GLN L 90 " pdb=" N GLU L 92 " model vdw 2.291 2.520 ... (remaining 29508 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.730 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3784 Z= 0.175 Angle : 0.465 5.767 5137 Z= 0.249 Chirality : 0.042 0.148 558 Planarity : 0.004 0.049 663 Dihedral : 8.421 50.903 1371 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.74 % Allowed : 3.71 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.94 (0.42), residues: 465 helix: -3.12 (0.74), residues: 33 sheet: -0.75 (0.46), residues: 156 loop : -0.08 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.001 0.001 HIS A 516 PHE 0.009 0.001 PHE A 426 TYR 0.009 0.001 TYR L 91 ARG 0.001 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9035 (tp) cc_final: 0.8645 (pt) REVERT: A 343 ARG cc_start: 0.9345 (mtt-85) cc_final: 0.9013 (ttm-80) REVERT: A 511 SER cc_start: 0.9440 (m) cc_final: 0.9192 (t) REVERT: A 532 LYS cc_start: 0.8724 (mttt) cc_final: 0.8496 (mttp) outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.2061 time to fit residues: 21.5888 Evaluate side-chains 67 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3784 Z= 0.169 Angle : 0.504 4.894 5137 Z= 0.271 Chirality : 0.043 0.145 558 Planarity : 0.004 0.044 663 Dihedral : 4.467 45.238 541 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.48 % Allowed : 11.39 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.54 (0.43), residues: 465 helix: -3.21 (0.89), residues: 28 sheet: -0.49 (0.45), residues: 152 loop : 0.17 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.002 0.001 HIS A 516 PHE 0.006 0.001 PHE A 562 TYR 0.019 0.001 TYR L 91 ARG 0.004 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9072 (tp) cc_final: 0.8675 (pt) REVERT: A 343 ARG cc_start: 0.9315 (mtt-85) cc_final: 0.8911 (ttm-80) REVERT: L 38 GLN cc_start: 0.8929 (tt0) cc_final: 0.8701 (tt0) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.2142 time to fit residues: 17.7917 Evaluate side-chains 65 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 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 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3784 Z= 0.287 Angle : 0.527 5.654 5137 Z= 0.282 Chirality : 0.045 0.161 558 Planarity : 0.004 0.044 663 Dihedral : 4.712 51.126 541 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.47 % Allowed : 12.13 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.73 (0.42), residues: 465 helix: -3.19 (0.90), residues: 28 sheet: -0.60 (0.44), residues: 152 loop : 0.00 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.012 0.001 PHE A 426 TYR 0.011 0.001 TYR L 94 ARG 0.002 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9086 (tp) cc_final: 0.8732 (pt) REVERT: A 343 ARG cc_start: 0.9288 (mtt-85) cc_final: 0.8954 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.1716 time to fit residues: 15.7983 Evaluate side-chains 71 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3784 Z= 0.217 Angle : 0.505 6.042 5137 Z= 0.267 Chirality : 0.044 0.150 558 Planarity : 0.004 0.041 663 Dihedral : 4.738 56.067 541 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.47 % Allowed : 13.86 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.78 (0.41), residues: 465 helix: -3.24 (0.84), residues: 29 sheet: -0.66 (0.43), residues: 152 loop : -0.00 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.012 0.001 TYR A 486 ARG 0.002 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9069 (tp) cc_final: 0.8717 (pt) REVERT: A 343 ARG cc_start: 0.9293 (mtt-85) cc_final: 0.9018 (ttm-80) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.2059 time to fit residues: 18.1158 Evaluate side-chains 72 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 39 optimal weight: 0.0970 chunk 10 optimal weight: 0.0030 chunk 14 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3784 Z= 0.137 Angle : 0.472 6.794 5137 Z= 0.250 Chirality : 0.043 0.137 558 Planarity : 0.003 0.041 663 Dihedral : 4.511 55.552 541 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.72 % Allowed : 15.59 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.59 (0.41), residues: 465 helix: -3.16 (0.82), residues: 29 sheet: -0.45 (0.43), residues: 152 loop : 0.08 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.007 0.001 PHE A 540 TYR 0.012 0.001 TYR A 486 ARG 0.004 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9028 (tp) cc_final: 0.8647 (pt) REVERT: A 343 ARG cc_start: 0.9304 (mtt-85) cc_final: 0.9081 (ttm-80) REVERT: A 564 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6195 (ptp90) outliers start: 11 outliers final: 6 residues processed: 70 average time/residue: 0.2147 time to fit residues: 17.8621 Evaluate side-chains 65 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3784 Z= 0.325 Angle : 0.544 5.224 5137 Z= 0.289 Chirality : 0.045 0.164 558 Planarity : 0.004 0.043 663 Dihedral : 4.722 52.645 541 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.21 % Allowed : 14.60 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.85 (0.40), residues: 465 helix: -3.00 (0.85), residues: 29 sheet: -0.65 (0.42), residues: 151 loop : -0.13 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 108 HIS 0.002 0.001 HIS A 516 PHE 0.013 0.001 PHE A 540 TYR 0.014 0.001 TYR A 486 ARG 0.002 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9058 (tp) cc_final: 0.8763 (pt) REVERT: A 343 ARG cc_start: 0.9295 (mtt-85) cc_final: 0.9000 (ttm-80) REVERT: A 564 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6244 (ptp90) outliers start: 17 outliers final: 13 residues processed: 70 average time/residue: 0.1838 time to fit residues: 15.7174 Evaluate side-chains 72 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3784 Z= 0.216 Angle : 0.511 7.210 5137 Z= 0.272 Chirality : 0.044 0.146 558 Planarity : 0.004 0.040 663 Dihedral : 4.466 46.835 541 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.70 % Allowed : 14.36 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.82 (0.40), residues: 465 helix: -3.00 (0.84), residues: 29 sheet: -0.68 (0.42), residues: 152 loop : -0.07 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.012 0.001 PHE A 540 TYR 0.015 0.001 TYR A 486 ARG 0.001 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9074 (tp) cc_final: 0.8769 (pt) REVERT: A 564 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6274 (ptp90) outliers start: 19 outliers final: 13 residues processed: 67 average time/residue: 0.1608 time to fit residues: 13.3310 Evaluate side-chains 66 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3784 Z= 0.304 Angle : 0.553 7.509 5137 Z= 0.294 Chirality : 0.045 0.159 558 Planarity : 0.004 0.041 663 Dihedral : 4.557 44.903 541 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.70 % Allowed : 14.85 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.00 (0.40), residues: 465 helix: -2.95 (0.86), residues: 29 sheet: -0.83 (0.42), residues: 151 loop : -0.20 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 108 HIS 0.002 0.001 HIS A 516 PHE 0.012 0.001 PHE A 426 TYR 0.015 0.001 TYR A 486 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9079 (tp) cc_final: 0.8799 (pt) REVERT: A 389 PHE cc_start: 0.8820 (m-80) cc_final: 0.8619 (m-80) REVERT: A 454 ARG cc_start: 0.8419 (ttt90) cc_final: 0.8218 (ttt-90) REVERT: A 564 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6314 (ptp90) outliers start: 19 outliers final: 16 residues processed: 66 average time/residue: 0.1493 time to fit residues: 12.5654 Evaluate side-chains 70 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3784 Z= 0.187 Angle : 0.520 9.172 5137 Z= 0.276 Chirality : 0.043 0.146 558 Planarity : 0.004 0.039 663 Dihedral : 4.167 35.902 541 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.96 % Allowed : 15.35 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.87 (0.40), residues: 465 helix: -2.92 (0.85), residues: 29 sheet: -0.74 (0.42), residues: 151 loop : -0.10 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 36 HIS 0.001 0.001 HIS A 516 PHE 0.007 0.001 PHE A 397 TYR 0.013 0.001 TYR A 486 ARG 0.002 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9069 (tp) cc_final: 0.8792 (pt) REVERT: A 389 PHE cc_start: 0.8776 (m-80) cc_final: 0.8529 (m-80) REVERT: A 564 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6309 (ptp90) REVERT: H 81 MET cc_start: 0.7450 (tmm) cc_final: 0.7193 (ttm) outliers start: 16 outliers final: 9 residues processed: 66 average time/residue: 0.1592 time to fit residues: 13.1820 Evaluate side-chains 64 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3784 Z= 0.228 Angle : 0.527 8.849 5137 Z= 0.281 Chirality : 0.044 0.149 558 Planarity : 0.004 0.040 663 Dihedral : 3.869 14.668 539 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.48 % Allowed : 17.33 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.87 (0.40), residues: 465 helix: -2.81 (0.88), residues: 29 sheet: -0.75 (0.42), residues: 151 loop : -0.11 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.013 0.001 TYR A 486 ARG 0.001 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 930 Ramachandran restraints generated. 465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ILE cc_start: 0.9074 (tp) cc_final: 0.8799 (pt) REVERT: A 389 PHE cc_start: 0.8797 (m-80) cc_final: 0.8588 (m-80) REVERT: A 564 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6319 (ptp90) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1587 time to fit residues: 11.9443 Evaluate side-chains 61 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 40 optimal weight: 0.0570 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN ** L 90 GLN ** 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 = 0.3729 r_free = 0.3729 target = 0.157222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.132024 restraints weight = 4326.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.132846 restraints weight = 3861.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133572 restraints weight = 3591.440| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3784 Z= 0.223 Angle : 0.520 8.524 5137 Z= 0.278 Chirality : 0.044 0.148 558 Planarity : 0.004 0.039 663 Dihedral : 3.874 14.585 539 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.47 % Allowed : 16.09 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -0.91 (0.40), residues: 465 helix: -2.81 (0.88), residues: 29 sheet: -0.74 (0.44), residues: 139 loop : -0.20 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 433 HIS 0.002 0.001 HIS A 516 PHE 0.008 0.001 PHE A 426 TYR 0.014 0.001 TYR A 486 ARG 0.002 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.69 seconds wall clock time: 26 minutes 22.86 seconds (1582.86 seconds total)