Starting phenix.real_space_refine on Sun Mar 10 15:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/03_2024/7tx7_26156_updated.pdb" } resolution = 3.8 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= 0.002 sd= 0.033 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 7 5.16 5 C 2158 2.51 5 N 487 2.21 5 O 551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3203 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3203 Unusual residues: {'AJP': 4} Classifications: {'peptide': 397, 'undetermined': 4} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 13, 'TRANS': 383, None: 4} Not linked: pdbres="GLN A 459 " pdbres="AJP A 701 " Not linked: pdbres="AJP A 701 " pdbres="AJP A 702 " Not linked: pdbres="AJP A 702 " pdbres="AJP A 703 " Not linked: pdbres="AJP A 703 " pdbres="AJP A 704 " Chain breaks: 1 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 543 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 2.49, per 1000 atoms: 0.78 Number of scatterers: 3203 At special positions: 0 Unit cell: (73.44, 65.88, 79.92, 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 7 16.00 O 551 8.00 N 487 7.00 C 2158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.34 Conformation dependent library (CDL) restraints added in 684.5 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.768A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.918A pdb=" N THR A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 61 through 89 removed outlier: 5.052A pdb=" N THR A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Proline residue: A 70 - end of helix removed outlier: 4.890A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.621A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.553A pdb=" N TYR A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.793A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 202 removed outlier: 4.104A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.644A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.015A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 3.672A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'A' and resid 359 through 390 removed outlier: 3.804A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.782A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 4.016A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 458 removed outlier: 3.515A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 597 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: 0.85 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 909 1.34 - 1.46: 569 1.46 - 1.57: 1817 1.57 - 1.69: 4 1.69 - 1.81: 11 Bond restraints: 3310 Sorted by residual: bond pdb=" C23 AJP A 703 " pdb=" C24 AJP A 703 " ideal model delta sigma weight residual 1.522 1.613 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C05 AJP A 704 " pdb=" C06 AJP A 704 " ideal model delta sigma weight residual 1.534 1.445 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C23 AJP A 704 " pdb=" C24 AJP A 704 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C23 AJP A 701 " pdb=" C24 AJP A 701 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C23 AJP A 702 " pdb=" C24 AJP A 702 " ideal model delta sigma weight residual 1.522 1.606 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 82 105.86 - 112.89: 1953 112.89 - 119.93: 1062 119.93 - 126.97: 1447 126.97 - 134.00: 39 Bond angle restraints: 4583 Sorted by residual: angle pdb=" N ALA A 131 " pdb=" CA ALA A 131 " pdb=" C ALA A 131 " ideal model delta sigma weight residual 111.28 116.70 -5.42 1.09e+00 8.42e-01 2.47e+01 angle pdb=" N ALA A 132 " pdb=" CA ALA A 132 " pdb=" C ALA A 132 " ideal model delta sigma weight residual 113.02 117.20 -4.18 1.20e+00 6.94e-01 1.21e+01 angle pdb=" C07 AJP A 701 " pdb=" C06 AJP A 701 " pdb=" C83 AJP A 701 " ideal model delta sigma weight residual 114.76 106.59 8.17 3.00e+00 1.11e-01 7.41e+00 angle pdb=" C07 AJP A 703 " pdb=" C06 AJP A 703 " pdb=" C83 AJP A 703 " ideal model delta sigma weight residual 114.76 107.70 7.06 3.00e+00 1.11e-01 5.53e+00 angle pdb=" C07 AJP A 702 " pdb=" C06 AJP A 702 " pdb=" C83 AJP A 702 " ideal model delta sigma weight residual 114.76 108.24 6.52 3.00e+00 1.11e-01 4.72e+00 ... (remaining 4578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.62: 2133 30.62 - 61.24: 54 61.24 - 91.85: 19 91.85 - 122.47: 19 122.47 - 153.09: 8 Dihedral angle restraints: 2233 sinusoidal: 1065 harmonic: 1168 Sorted by residual: dihedral pdb=" O31 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual 177.28 -29.63 -153.09 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C29 AJP A 702 " pdb=" C30 AJP A 702 " pdb=" C32 AJP A 702 " pdb=" O33 AJP A 702 " ideal model delta sinusoidal sigma weight residual -60.96 90.80 -151.76 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C21 AJP A 704 " pdb=" C22 AJP A 704 " pdb=" C23 AJP A 704 " pdb=" O25 AJP A 704 " ideal model delta sinusoidal sigma weight residual 176.32 50.06 126.26 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 2230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 499 0.064 - 0.128: 50 0.128 - 0.192: 8 0.192 - 0.256: 13 0.256 - 0.320: 15 Chirality restraints: 585 Sorted by residual: chirality pdb=" C19 AJP A 702 " pdb=" C18 AJP A 702 " pdb=" C20 AJP A 702 " pdb=" C24 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C11 AJP A 702 " pdb=" C10 AJP A 702 " pdb=" C12 AJP A 702 " pdb=" C16 AJP A 702 " both_signs ideal model delta sigma weight residual False 2.20 2.52 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C11 AJP A 704 " pdb=" C10 AJP A 704 " pdb=" C12 AJP A 704 " pdb=" C16 AJP A 704 " both_signs ideal model delta sigma weight residual False 2.20 2.51 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 582 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 94 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO A 43 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 205 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 206 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.019 5.00e-02 4.00e+02 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 29 2.64 - 3.20: 3285 3.20 - 3.77: 4940 3.77 - 4.33: 6169 4.33 - 4.90: 10235 Nonbonded interactions: 24658 Sorted by model distance: nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.072 2.440 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.270 2.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.279 2.440 nonbonded pdb=" ND1 HIS A 289 " pdb=" OD1 ASN A 306 " model vdw 2.410 2.520 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.421 2.440 ... (remaining 24653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 0.000 Extract box with map and model: 1.770 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.008 0.091 3310 Z= 0.481 Angle : 0.760 8.165 4583 Z= 0.336 Chirality : 0.068 0.320 585 Planarity : 0.005 0.061 518 Dihedral : 21.146 153.091 1483 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % 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: 3.77 (0.42), residues: 393 helix: 3.08 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -0.26 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 118 PHE 0.007 0.001 PHE A 405 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.336 Fit side-chains REVERT: A 51 TYR cc_start: 0.8750 (t80) cc_final: 0.8369 (t80) REVERT: A 133 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8280 (mpt-90) REVERT: A 195 PHE cc_start: 0.7125 (t80) cc_final: 0.6548 (t80) REVERT: A 300 ASN cc_start: 0.8397 (t0) cc_final: 0.8129 (t0) REVERT: A 305 TYR cc_start: 0.7633 (m-80) cc_final: 0.7299 (m-80) REVERT: A 431 GLN cc_start: 0.8145 (tt0) cc_final: 0.7930 (tt0) REVERT: A 440 LEU cc_start: 0.8233 (tt) cc_final: 0.8023 (tp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1644 time to fit residues: 25.2445 Evaluate side-chains 103 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.0570 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 277 ASN A 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3310 Z= 0.186 Angle : 0.734 7.858 4583 Z= 0.326 Chirality : 0.038 0.171 585 Planarity : 0.005 0.050 518 Dihedral : 11.854 121.800 891 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.95 % Allowed : 17.92 % Favored : 80.13 % 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: 3.25 (0.42), residues: 393 helix: 2.60 (0.28), residues: 327 sheet: None (None), residues: 0 loop : -0.24 (0.82), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 118 PHE 0.017 0.001 PHE A 351 TYR 0.013 0.001 TYR A 366 ARG 0.005 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8741 (t80) cc_final: 0.8236 (t80) REVERT: A 195 PHE cc_start: 0.7268 (t80) cc_final: 0.6469 (t80) REVERT: A 291 LEU cc_start: 0.9305 (tp) cc_final: 0.9086 (tp) REVERT: A 300 ASN cc_start: 0.8297 (t0) cc_final: 0.8009 (t0) REVERT: A 431 GLN cc_start: 0.8064 (tt0) cc_final: 0.7831 (tt0) outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.1273 time to fit residues: 18.5715 Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.0470 chunk 18 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3310 Z= 0.175 Angle : 0.615 6.929 4583 Z= 0.291 Chirality : 0.035 0.113 585 Planarity : 0.005 0.047 518 Dihedral : 7.557 70.281 891 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.61 % Allowed : 20.20 % Favored : 77.20 % 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: 2.79 (0.43), residues: 393 helix: 2.39 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.46 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 PHE 0.014 0.001 PHE A 103 TYR 0.014 0.001 TYR A 35 ARG 0.004 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.367 Fit side-chains REVERT: A 51 TYR cc_start: 0.8718 (t80) cc_final: 0.8254 (t80) REVERT: A 133 ARG cc_start: 0.8482 (mtt180) cc_final: 0.7811 (mtt90) REVERT: A 195 PHE cc_start: 0.7147 (t80) cc_final: 0.6367 (t80) REVERT: A 300 ASN cc_start: 0.8243 (t0) cc_final: 0.7860 (t0) REVERT: A 336 LYS cc_start: 0.8374 (mttt) cc_final: 0.8063 (mmtm) REVERT: A 391 LEU cc_start: 0.8771 (pp) cc_final: 0.8446 (pp) REVERT: A 431 GLN cc_start: 0.8177 (tt0) cc_final: 0.7974 (mt0) outliers start: 8 outliers final: 6 residues processed: 110 average time/residue: 0.1202 time to fit residues: 16.5687 Evaluate side-chains 99 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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: 0.7470 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3310 Z= 0.158 Angle : 0.571 6.466 4583 Z= 0.275 Chirality : 0.034 0.113 585 Planarity : 0.004 0.045 518 Dihedral : 5.971 52.895 891 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.26 % Allowed : 21.17 % Favored : 75.57 % 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: 2.66 (0.43), residues: 393 helix: 2.27 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.61 (0.73), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.016 0.001 PHE A 378 TYR 0.018 0.001 TYR A 136 ARG 0.003 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.366 Fit side-chains REVERT: A 51 TYR cc_start: 0.8711 (t80) cc_final: 0.8228 (t80) REVERT: A 133 ARG cc_start: 0.8479 (mtt180) cc_final: 0.7810 (mtt90) REVERT: A 195 PHE cc_start: 0.7161 (t80) cc_final: 0.6446 (t80) REVERT: A 300 ASN cc_start: 0.8342 (t0) cc_final: 0.8084 (t0) REVERT: A 336 LYS cc_start: 0.8345 (mttt) cc_final: 0.8081 (mmtm) REVERT: A 391 LEU cc_start: 0.8821 (pp) cc_final: 0.8544 (pp) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.1252 time to fit residues: 17.1484 Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 32 optimal weight: 0.0070 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3310 Z= 0.210 Angle : 0.585 6.207 4583 Z= 0.290 Chirality : 0.035 0.122 585 Planarity : 0.005 0.044 518 Dihedral : 5.787 51.404 891 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.89 % Allowed : 19.87 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.43), residues: 393 helix: 2.29 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.88 (0.72), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 358 PHE 0.018 0.001 PHE A 103 TYR 0.014 0.001 TYR A 136 ARG 0.003 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.397 Fit side-chains REVERT: A 51 TYR cc_start: 0.8731 (t80) cc_final: 0.8282 (t80) REVERT: A 133 ARG cc_start: 0.8525 (mtt180) cc_final: 0.7866 (mtt90) REVERT: A 195 PHE cc_start: 0.7225 (t80) cc_final: 0.6472 (t80) REVERT: A 300 ASN cc_start: 0.8366 (t0) cc_final: 0.8135 (t0) REVERT: A 336 LYS cc_start: 0.8430 (mttt) cc_final: 0.8137 (mmtm) REVERT: A 338 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8209 (tt) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.1237 time to fit residues: 15.9797 Evaluate side-chains 99 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3310 Z= 0.183 Angle : 0.612 7.965 4583 Z= 0.292 Chirality : 0.035 0.188 585 Planarity : 0.004 0.042 518 Dihedral : 5.603 51.097 891 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.58 % Allowed : 24.76 % Favored : 71.66 % 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: 2.46 (0.43), residues: 393 helix: 2.22 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.16 (0.69), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.015 0.001 PHE A 326 TYR 0.015 0.001 TYR A 136 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.371 Fit side-chains REVERT: A 51 TYR cc_start: 0.8655 (t80) cc_final: 0.8086 (t80) REVERT: A 133 ARG cc_start: 0.8548 (mtt180) cc_final: 0.7853 (mtt90) REVERT: A 195 PHE cc_start: 0.7226 (t80) cc_final: 0.6482 (t80) REVERT: A 300 ASN cc_start: 0.8319 (t0) cc_final: 0.8118 (t0) REVERT: A 336 LYS cc_start: 0.8341 (mttt) cc_final: 0.8067 (mmtm) REVERT: A 338 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8173 (tt) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.1246 time to fit residues: 14.8501 Evaluate side-chains 98 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 19 optimal weight: 10.0000 overall best weight: 0.3670 ------------------------------------------------------------------------------- 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: 0.7495 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3310 Z= 0.163 Angle : 0.617 10.141 4583 Z= 0.289 Chirality : 0.035 0.143 585 Planarity : 0.004 0.041 518 Dihedral : 5.349 50.506 891 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.61 % Allowed : 26.06 % Favored : 71.34 % 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: 2.43 (0.43), residues: 393 helix: 2.15 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.92 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.029 0.001 PHE A 322 TYR 0.020 0.001 TYR A 136 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.345 Fit side-chains REVERT: A 51 TYR cc_start: 0.8639 (t80) cc_final: 0.8096 (t80) REVERT: A 101 LEU cc_start: 0.8910 (mt) cc_final: 0.8690 (mp) REVERT: A 133 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7808 (mtt90) REVERT: A 305 TYR cc_start: 0.7994 (m-80) cc_final: 0.7645 (m-80) REVERT: A 336 LYS cc_start: 0.8275 (mttt) cc_final: 0.8029 (mmtm) REVERT: A 338 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.1269 time to fit residues: 15.4548 Evaluate side-chains 92 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7511 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3310 Z= 0.177 Angle : 0.659 9.516 4583 Z= 0.300 Chirality : 0.036 0.149 585 Planarity : 0.004 0.040 518 Dihedral : 5.308 49.569 891 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.61 % Allowed : 26.38 % Favored : 71.01 % 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: 2.41 (0.43), residues: 393 helix: 2.16 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -1.10 (0.72), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 PHE 0.025 0.002 PHE A 103 TYR 0.019 0.001 TYR A 136 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.345 Fit side-chains REVERT: A 51 TYR cc_start: 0.8637 (t80) cc_final: 0.8086 (t80) REVERT: A 101 LEU cc_start: 0.8900 (mt) cc_final: 0.8695 (mp) REVERT: A 133 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8128 (mtp85) REVERT: A 305 TYR cc_start: 0.8115 (m-80) cc_final: 0.7767 (m-80) REVERT: A 336 LYS cc_start: 0.8323 (mttt) cc_final: 0.8060 (mmtm) REVERT: A 338 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8168 (tt) outliers start: 8 outliers final: 6 residues processed: 94 average time/residue: 0.1428 time to fit residues: 16.5013 Evaluate side-chains 94 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7511 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3310 Z= 0.176 Angle : 0.657 9.362 4583 Z= 0.302 Chirality : 0.035 0.129 585 Planarity : 0.004 0.040 518 Dihedral : 5.210 49.007 891 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.61 % Allowed : 26.71 % Favored : 70.68 % 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: 2.45 (0.43), residues: 393 helix: 2.21 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.10 (0.70), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.030 0.002 PHE A 322 TYR 0.019 0.001 TYR A 136 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.359 Fit side-chains REVERT: A 51 TYR cc_start: 0.8615 (t80) cc_final: 0.8049 (t80) REVERT: A 101 LEU cc_start: 0.8848 (mt) cc_final: 0.8634 (mp) REVERT: A 294 GLU cc_start: 0.8061 (tp30) cc_final: 0.7824 (tp30) REVERT: A 305 TYR cc_start: 0.8111 (m-80) cc_final: 0.7754 (m-80) REVERT: A 336 LYS cc_start: 0.8305 (mttt) cc_final: 0.8037 (mmtm) outliers start: 8 outliers final: 7 residues processed: 96 average time/residue: 0.1272 time to fit residues: 15.4152 Evaluate side-chains 94 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7541 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3310 Z= 0.205 Angle : 0.679 9.198 4583 Z= 0.315 Chirality : 0.036 0.153 585 Planarity : 0.004 0.039 518 Dihedral : 5.321 48.527 891 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.28 % Allowed : 28.01 % Favored : 69.71 % 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: 2.37 (0.43), residues: 393 helix: 2.17 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.21 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 PHE 0.018 0.001 PHE A 103 TYR 0.019 0.001 TYR A 136 ARG 0.005 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.343 Fit side-chains REVERT: A 286 TYR cc_start: 0.8774 (m-10) cc_final: 0.8555 (m-10) REVERT: A 336 LYS cc_start: 0.8402 (mttt) cc_final: 0.8126 (mmtm) outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 0.1283 time to fit residues: 14.5024 Evaluate side-chains 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.0030 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124897 restraints weight = 6021.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128566 restraints weight = 3242.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131006 restraints weight = 1979.329| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3310 Z= 0.185 Angle : 0.703 9.103 4583 Z= 0.321 Chirality : 0.036 0.128 585 Planarity : 0.004 0.040 518 Dihedral : 5.196 48.265 891 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.28 % Allowed : 28.34 % Favored : 69.38 % 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: 2.33 (0.43), residues: 393 helix: 2.12 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.13 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.016 0.001 PHE A 326 TYR 0.020 0.002 TYR A 376 ARG 0.002 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.19 seconds wall clock time: 20 minutes 19.08 seconds (1219.08 seconds total)