Starting phenix.real_space_refine on Mon Sep 23 15:40:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/09_2024/7tx7_26156.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/09_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_26156/09_2024/7tx7_26156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/09_2024/7tx7_26156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/09_2024/7tx7_26156.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx7_26156/09_2024/7tx7_26156.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3203 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3042 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 7 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 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'AJP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 81 Time building chain proxies: 2.73, per 1000 atoms: 0.85 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 376.3 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... Secondary structure from input PDB file: 17 helices and 0 sheets defined 88.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.990A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) 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 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 90 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 91 through 113 removed outlier: 3.958A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.621A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.742A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 179 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 181 through 203 removed outlier: 4.104A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (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 264 through 296 removed outlier: 4.147A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) 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 305 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 335 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.646A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 4.516A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 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 427 through 459 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) removed outlier: 4.147A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 732 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: 0.82 Time building geometry restraints manager: 1.03 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: 0.00 - 1.63: 4384 1.63 - 3.27: 138 3.27 - 4.90: 46 4.90 - 6.53: 13 6.53 - 8.17: 2 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: 28 2.64 - 3.20: 3257 3.20 - 3.77: 4947 3.77 - 4.33: 6145 4.33 - 4.90: 10221 Nonbonded interactions: 24598 Sorted by model distance: nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.072 3.040 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.270 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.279 3.040 nonbonded pdb=" ND1 HIS A 289 " pdb=" OD1 ASN A 306 " model vdw 2.410 3.120 nonbonded pdb=" O TYR A 126 " pdb=" OG1 THR A 129 " model vdw 2.421 3.040 ... (remaining 24593 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: 0.330 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- 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= 0.501 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 : 0.332 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: 0.1676 time to fit residues: 25.8156 Evaluate side-chains 103 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2527 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= 0.205 Angle : 0.734 7.750 4583 Z= 0.331 Chirality : 0.040 0.203 585 Planarity : 0.004 0.051 518 Dihedral : 12.620 127.437 891 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 1.95 % Allowed : 17.59 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.43), residues: 393 helix: 3.00 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -0.13 (0.85), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 PHE 0.018 0.002 PHE A 351 TYR 0.015 0.002 TYR A 366 ARG 0.006 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 116 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.362 Fit side-chains REVERT: A 51 TYR cc_start: 0.8794 (t80) cc_final: 0.8066 (t80) REVERT: A 133 ARG cc_start: 0.8433 (mtt180) cc_final: 0.7601 (mtt90) REVERT: A 195 PHE cc_start: 0.7333 (t80) cc_final: 0.6515 (t80) REVERT: A 300 ASN cc_start: 0.8274 (t0) cc_final: 0.8013 (t0) REVERT: A 431 GLN cc_start: 0.8188 (tt0) cc_final: 0.7971 (tt0) outliers start: 6 outliers final: 6 residues processed: 113 average time/residue: 0.1241 time to fit residues: 17.3283 Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3258 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= 0.180 Angle : 0.620 6.706 4583 Z= 0.295 Chirality : 0.037 0.121 585 Planarity : 0.004 0.048 518 Dihedral : 10.103 131.372 891 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 19.87 % Favored : 77.85 % 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: 3.81 (0.43), residues: 393 helix: 3.03 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.20 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 118 PHE 0.015 0.001 PHE A 103 TYR 0.015 0.001 TYR A 366 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 107 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.358 Fit side-chains REVERT: A 34 PHE cc_start: 0.8987 (t80) cc_final: 0.8770 (t80) REVERT: A 51 TYR cc_start: 0.8702 (t80) cc_final: 0.7947 (t80) REVERT: A 133 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7573 (mtt90) REVERT: A 195 PHE cc_start: 0.7179 (t80) cc_final: 0.6422 (t80) REVERT: A 300 ASN cc_start: 0.8212 (t0) cc_final: 0.7976 (t0) REVERT: A 336 LYS cc_start: 0.8349 (mttt) cc_final: 0.8071 (mmtm) REVERT: A 431 GLN cc_start: 0.8160 (tt0) cc_final: 0.7932 (tt0) outliers start: 7 outliers final: 5 residues processed: 105 average time/residue: 0.1236 time to fit residues: 16.1881 Evaluate side-chains 97 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3310 Z= 0.189 Angle : 0.608 8.296 4583 Z= 0.289 Chirality : 0.036 0.119 585 Planarity : 0.004 0.045 518 Dihedral : 8.956 110.680 891 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.56 % Allowed : 16.94 % Favored : 78.50 % 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: 3.64 (0.43), residues: 393 helix: 2.91 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -0.57 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 289 PHE 0.014 0.001 PHE A 326 TYR 0.019 0.002 TYR A 366 ARG 0.003 0.000 ARG A 61 *********************** 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 110 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9047 (tt0) cc_final: 0.8545 (tt0) REVERT: A 51 TYR cc_start: 0.8722 (t80) cc_final: 0.8083 (t80) REVERT: A 195 PHE cc_start: 0.7149 (t80) cc_final: 0.6361 (t80) REVERT: A 336 LYS cc_start: 0.8355 (mttt) cc_final: 0.8073 (mmtm) REVERT: A 338 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 411 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7720 (ttmt) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.1218 time to fit residues: 16.0690 Evaluate side-chains 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 137 SER 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 364 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3310 Z= 0.190 Angle : 0.622 7.244 4583 Z= 0.302 Chirality : 0.036 0.112 585 Planarity : 0.004 0.042 518 Dihedral : 6.518 52.536 891 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.23 % Allowed : 18.89 % Favored : 76.87 % 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: 3.43 (0.43), residues: 393 helix: 2.80 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -0.90 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.001 0.001 HIS A 355 PHE 0.027 0.002 PHE A 34 TYR 0.023 0.002 TYR A 366 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 110 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.318 Fit side-chains REVERT: A 45 GLU cc_start: 0.9000 (tt0) cc_final: 0.8446 (tt0) REVERT: A 51 TYR cc_start: 0.8718 (t80) cc_final: 0.8035 (t80) REVERT: A 195 PHE cc_start: 0.7209 (t80) cc_final: 0.6526 (t80) REVERT: A 336 LYS cc_start: 0.8353 (mttt) cc_final: 0.8078 (mmtm) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.1291 time to fit residues: 16.7743 Evaluate side-chains 98 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.0470 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3310 Z= 0.185 Angle : 0.648 8.869 4583 Z= 0.311 Chirality : 0.037 0.190 585 Planarity : 0.004 0.043 518 Dihedral : 5.573 52.161 891 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.26 % Allowed : 23.13 % Favored : 73.62 % 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: 3.33 (0.43), residues: 393 helix: 2.72 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.96 (0.80), residues: 60 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 0.020 0.001 PHE A 34 TYR 0.027 0.002 TYR A 366 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 107 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8927 (tt0) cc_final: 0.8544 (tt0) REVERT: A 51 TYR cc_start: 0.8707 (t80) cc_final: 0.8105 (t80) REVERT: A 97 LEU cc_start: 0.8587 (tp) cc_final: 0.8307 (tp) REVERT: A 300 ASN cc_start: 0.7857 (t0) cc_final: 0.6739 (m-40) REVERT: A 336 LYS cc_start: 0.8322 (mttt) cc_final: 0.8073 (mmtm) REVERT: A 338 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8161 (tt) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1228 time to fit residues: 15.8997 Evaluate side-chains 96 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.0070 chunk 18 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3310 Z= 0.196 Angle : 0.681 13.131 4583 Z= 0.326 Chirality : 0.038 0.173 585 Planarity : 0.004 0.040 518 Dihedral : 5.395 52.012 891 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.23 % Allowed : 23.13 % Favored : 72.64 % 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: 3.17 (0.43), residues: 393 helix: 2.62 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.06 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 PHE 0.025 0.001 PHE A 322 TYR 0.007 0.001 TYR A 35 ARG 0.003 0.000 ARG A 61 *********************** 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 109 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.402 Fit side-chains REVERT: A 51 TYR cc_start: 0.8672 (t80) cc_final: 0.8155 (t80) REVERT: A 59 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: A 133 ARG cc_start: 0.8458 (mtt180) cc_final: 0.7940 (mtt90) REVERT: A 294 GLU cc_start: 0.8051 (tp30) cc_final: 0.7841 (tp30) REVERT: A 300 ASN cc_start: 0.7931 (t0) cc_final: 0.6829 (m-40) REVERT: A 336 LYS cc_start: 0.8316 (mttt) cc_final: 0.8071 (mmtm) REVERT: A 338 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8168 (tt) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.1291 time to fit residues: 16.7264 Evaluate side-chains 100 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 190 LEU 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 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3310 Z= 0.178 Angle : 0.700 16.295 4583 Z= 0.326 Chirality : 0.038 0.185 585 Planarity : 0.004 0.039 518 Dihedral : 5.186 51.860 891 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.93 % Allowed : 25.08 % Favored : 71.99 % 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: 3.23 (0.43), residues: 393 helix: 2.59 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -0.86 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 PHE 0.031 0.002 PHE A 34 TYR 0.037 0.001 TYR A 366 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: 9 poor density : 89 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8650 (t80) cc_final: 0.8192 (t80) REVERT: A 286 TYR cc_start: 0.8837 (m-10) cc_final: 0.8613 (m-10) REVERT: A 294 GLU cc_start: 0.7957 (tp30) cc_final: 0.7729 (tp30) REVERT: A 300 ASN cc_start: 0.7859 (t0) cc_final: 0.6720 (m-40) REVERT: A 336 LYS cc_start: 0.8314 (mttt) cc_final: 0.8091 (mmtm) REVERT: A 338 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (tt) outliers start: 9 outliers final: 6 residues processed: 94 average time/residue: 0.1328 time to fit residues: 15.4725 Evaluate side-chains 93 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3310 Z= 0.219 Angle : 0.702 15.018 4583 Z= 0.337 Chirality : 0.038 0.182 585 Planarity : 0.004 0.038 518 Dihedral : 5.328 50.748 891 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.93 % Allowed : 25.08 % Favored : 71.99 % 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: 3.17 (0.43), residues: 393 helix: 2.56 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.01 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 270 HIS 0.002 0.001 HIS A 355 PHE 0.033 0.002 PHE A 322 TYR 0.034 0.002 TYR A 366 ARG 0.004 0.000 ARG A 61 *********************** 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: 9 poor density : 91 time to evaluate : 0.350 Fit side-chains REVERT: A 42 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7855 (mtm-85) REVERT: A 51 TYR cc_start: 0.8740 (t80) cc_final: 0.8256 (t80) REVERT: A 59 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: A 336 LYS cc_start: 0.8361 (mttt) cc_final: 0.8094 (mmtm) REVERT: A 338 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8185 (tt) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.1384 time to fit residues: 16.3189 Evaluate side-chains 96 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3310 Z= 0.189 Angle : 0.721 15.434 4583 Z= 0.339 Chirality : 0.038 0.191 585 Planarity : 0.004 0.038 518 Dihedral : 5.154 50.711 891 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 3.18 (0.43), residues: 393 helix: 2.55 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -0.90 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.001 HIS A 355 PHE 0.028 0.001 PHE A 34 TYR 0.010 0.001 TYR A 92 ARG 0.002 0.000 ARG A 151 ********************** 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 95 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.364 Fit side-chains REVERT: A 42 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: A 51 TYR cc_start: 0.8701 (t80) cc_final: 0.8219 (t80) REVERT: A 59 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: A 286 TYR cc_start: 0.8845 (m-10) cc_final: 0.8625 (m-10) REVERT: A 300 ASN cc_start: 0.7877 (t0) cc_final: 0.6866 (m-40) REVERT: A 336 LYS cc_start: 0.8340 (mttt) cc_final: 0.8106 (mmtm) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.1466 time to fit residues: 16.4304 Evaluate side-chains 93 residues out of total 341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126013 restraints weight = 5976.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129736 restraints weight = 3226.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132243 restraints weight = 1974.121| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 3310 Z= 0.208 Angle : 0.720 14.753 4583 Z= 0.341 Chirality : 0.038 0.186 585 Planarity : 0.004 0.038 518 Dihedral : 5.182 49.937 891 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.95 % Allowed : 27.69 % Favored : 70.36 % 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: 3.12 (0.43), residues: 393 helix: 2.50 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -0.90 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 355 PHE 0.027 0.001 PHE A 34 TYR 0.036 0.002 TYR A 366 ARG 0.003 0.000 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1048.71 seconds wall clock time: 19 minutes 16.57 seconds (1156.57 seconds total)