Starting phenix.real_space_refine on Wed Jul 1 22:36:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tx7_26156/07_2026/7tx7_26156.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ARG:plan': 11, 'GLU:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} 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: 4 Unresolved non-hydrogen chiralities: 81 Time building chain proxies: 1.11, per 1000 atoms: 0.35 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: 0.35 Conformation dependent library (CDL) restraints added in 120.1 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: 0.08 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: 0.50 Time building geometry restraints manager: 0.45 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 - 24.78: 1738 24.78 - 49.56: 46 49.56 - 74.35: 3 74.35 - 99.13: 0 99.13 - 123.91: 4 Dihedral angle restraints: 1791 sinusoidal: 623 harmonic: 1168 Sorted by residual: dihedral pdb=" C02 AJP A 703 " pdb=" C85 AJP A 703 " pdb=" O84 AJP A 703 " pdb=" C05 AJP A 703 " ideal model delta sinusoidal sigma weight residual -57.60 66.31 -123.91 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C02 AJP A 704 " pdb=" C85 AJP A 704 " pdb=" O84 AJP A 704 " pdb=" C05 AJP A 704 " ideal model delta sinusoidal sigma weight residual -57.60 66.29 -123.89 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C02 AJP A 701 " pdb=" C85 AJP A 701 " pdb=" O84 AJP A 701 " pdb=" C05 AJP A 701 " ideal model delta sinusoidal sigma weight residual -57.60 63.25 -120.85 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 1788 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: 0.510 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.440 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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= 0.402 Angle : 0.760 8.165 4583 Z= 0.336 Chirality : 0.068 0.320 585 Planarity : 0.005 0.061 518 Dihedral : 12.936 123.910 1041 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.71 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG A 268 TYR 0.011 0.001 TYR A 35 PHE 0.007 0.001 PHE A 405 TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.40 ( 3310) covalent geometry : angle 0.76037 / 0.34 ( 4583) hydrogen bonds : bond 0.14491 / 9.52 ( 244) hydrogen bonds : angle 5.44710 / 4.22 ( 732) *********************** 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 to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.120 Fit side-chains REVERT: A 51 TYR cc_start: 0.8750 (t80) cc_final: 0.8368 (t80) REVERT: A 133 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8282 (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: 0.8127 (t0) REVERT: A 305 TYR cc_start: 0.7633 (m-80) cc_final: 0.7300 (m-80) REVERT: A 431 GLN cc_start: 0.8144 (tt0) cc_final: 0.7930 (tt0) REVERT: A 440 LEU cc_start: 0.8233 (tt) cc_final: 0.8025 (tp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0746 time to fit residues: 11.5614 Evaluate side-chains 103 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125508 restraints weight = 5964.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.129245 restraints weight = 3230.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131866 restraints weight = 1976.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133585 restraints weight = 1303.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134785 restraints weight = 915.101| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2432 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= 0.157 Angle : 0.712 7.423 4583 Z= 0.327 Chirality : 0.039 0.156 585 Planarity : 0.004 0.052 518 Dihedral : 9.514 109.590 449 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.95 % Allowed : 17.26 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.91 (0.43), residues: 393 helix: 3.00 (0.28), residues: 328 sheet: None (None), residues: 0 loop : 0.26 (0.90), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 151 TYR 0.014 0.002 TYR A 366 PHE 0.017 0.002 PHE A 351 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 3310) covalent geometry : angle 0.71231 / 0.33 ( 4583) hydrogen bonds : bond 0.05253 / 3.52 ( 244) hydrogen bonds : angle 4.28253 / 3.30 ( 732) *********************** 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 112 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.098 Fit side-chains REVERT: A 51 TYR cc_start: 0.8828 (t80) cc_final: 0.8143 (t80) REVERT: A 130 MET cc_start: 0.8587 (ttm) cc_final: 0.8359 (mtm) REVERT: A 133 ARG cc_start: 0.8382 (mtt180) cc_final: 0.7022 (mpt-90) REVERT: A 195 PHE cc_start: 0.7403 (t80) cc_final: 0.6594 (t80) REVERT: A 300 ASN cc_start: 0.8322 (t0) cc_final: 0.8059 (t0) REVERT: A 431 GLN cc_start: 0.8048 (tt0) cc_final: 0.7627 (mt0) outliers start: 6 outliers final: 6 residues processed: 109 average time/residue: 0.0501 time to fit residues: 6.9651 Evaluate side-chains 99 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126365 restraints weight = 5934.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130270 restraints weight = 3189.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132848 restraints weight = 1930.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134652 restraints weight = 1276.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135926 restraints weight = 893.830| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3310 Z= 0.129 Angle : 0.641 6.844 4583 Z= 0.296 Chirality : 0.037 0.123 585 Planarity : 0.004 0.047 518 Dihedral : 9.611 109.628 449 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.61 % Allowed : 19.22 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.43), residues: 393 helix: 3.07 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.27 (0.82), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.020 0.001 TYR A 366 PHE 0.015 0.001 PHE A 103 TRP 0.006 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 3310) covalent geometry : angle 0.64148 / 0.30 ( 4583) hydrogen bonds : bond 0.04578 / 3.06 ( 244) hydrogen bonds : angle 3.81927 / 2.95 ( 732) *********************** 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 108 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.114 Fit side-chains REVERT: A 32 LEU cc_start: 0.8584 (mp) cc_final: 0.8381 (tp) REVERT: A 34 PHE cc_start: 0.8905 (t80) cc_final: 0.8704 (t80) REVERT: A 51 TYR cc_start: 0.8712 (t80) cc_final: 0.7976 (t80) REVERT: A 119 MET cc_start: 0.8310 (mmm) cc_final: 0.8082 (mmm) REVERT: A 133 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7642 (mtt90) REVERT: A 172 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: A 195 PHE cc_start: 0.7231 (t80) cc_final: 0.6460 (t80) REVERT: A 300 ASN cc_start: 0.8173 (t0) cc_final: 0.7773 (t0) REVERT: A 336 LYS cc_start: 0.8318 (mttt) cc_final: 0.8034 (mmtm) REVERT: A 431 GLN cc_start: 0.7912 (tt0) cc_final: 0.7657 (mt0) outliers start: 8 outliers final: 5 residues processed: 105 average time/residue: 0.0572 time to fit residues: 7.4996 Evaluate side-chains 91 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 172 GLN Chi-restraints excluded: chain A residue 190 LEU 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 7 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3733 r_free = 0.3733 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124675 restraints weight = 5960.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128441 restraints weight = 3239.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130988 restraints weight = 1978.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132789 restraints weight = 1309.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.134079 restraints weight = 917.211| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3310 Z= 0.145 Angle : 0.647 7.460 4583 Z= 0.305 Chirality : 0.037 0.128 585 Planarity : 0.004 0.044 518 Dihedral : 9.623 110.570 449 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.58 % Allowed : 19.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.43), residues: 393 helix: 2.88 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -0.45 (0.85), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 151 TYR 0.015 0.001 TYR A 35 PHE 0.014 0.001 PHE A 326 TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 3310) covalent geometry : angle 0.64664 / 0.30 ( 4583) hydrogen bonds : bond 0.04494 / 3.06 ( 244) hydrogen bonds : angle 3.85487 / 2.95 ( 732) *********************** 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 100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.072 Fit side-chains REVERT: A 34 PHE cc_start: 0.8968 (t80) cc_final: 0.8766 (t80) REVERT: A 51 TYR cc_start: 0.8724 (t80) cc_final: 0.8051 (t80) REVERT: A 119 MET cc_start: 0.8105 (mmm) cc_final: 0.7899 (mmm) REVERT: A 133 ARG cc_start: 0.8382 (mtt180) cc_final: 0.7635 (mtt90) REVERT: A 195 PHE cc_start: 0.7199 (t80) cc_final: 0.6442 (t80) REVERT: A 300 ASN cc_start: 0.8197 (t0) cc_final: 0.7859 (t0) REVERT: A 336 LYS cc_start: 0.8374 (mttt) cc_final: 0.8074 (mmtm) REVERT: A 431 GLN cc_start: 0.8028 (tt0) cc_final: 0.7718 (mt0) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.0448 time to fit residues: 5.5003 Evaluate side-chains 94 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 LEU 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 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.0050 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3758 r_free = 0.3758 target = 0.140069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125897 restraints weight = 5926.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129768 restraints weight = 3241.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.132335 restraints weight = 1979.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134161 restraints weight = 1321.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135496 restraints weight = 926.344| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3722 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= 0.124 Angle : 0.635 9.039 4583 Z= 0.296 Chirality : 0.036 0.177 585 Planarity : 0.004 0.042 518 Dihedral : 9.578 109.184 449 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.93 % Allowed : 19.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.43), residues: 393 helix: 2.80 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.59 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.014 0.001 TYR A 35 PHE 0.022 0.001 PHE A 103 TRP 0.006 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 3310) covalent geometry : angle 0.63455 / 0.30 ( 4583) hydrogen bonds : bond 0.04250 / 2.92 ( 244) hydrogen bonds : angle 3.70899 / 2.85 ( 732) *********************** 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 104 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8668 (t80) cc_final: 0.7990 (t80) REVERT: A 101 LEU cc_start: 0.8884 (mt) cc_final: 0.8671 (mp) REVERT: A 195 PHE cc_start: 0.7181 (t80) cc_final: 0.6406 (t80) REVERT: A 300 ASN cc_start: 0.8224 (t0) cc_final: 0.7952 (t0) REVERT: A 336 LYS cc_start: 0.8319 (mttt) cc_final: 0.8061 (mmtm) REVERT: A 338 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8077 (tt) REVERT: A 431 GLN cc_start: 0.8066 (tt0) cc_final: 0.7806 (mt0) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.0599 time to fit residues: 7.5265 Evaluate side-chains 98 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS 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 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 15 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3749 r_free = 0.3749 target = 0.139245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125100 restraints weight = 5929.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128914 restraints weight = 3252.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131429 restraints weight = 2010.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.133325 restraints weight = 1339.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134577 restraints weight = 932.616| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4019 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= 0.133 Angle : 0.644 6.946 4583 Z= 0.305 Chirality : 0.038 0.225 585 Planarity : 0.004 0.042 518 Dihedral : 9.563 109.494 449 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.23 % Allowed : 21.50 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.43), residues: 393 helix: 2.70 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.70 (0.83), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.009 0.001 TYR A 35 PHE 0.023 0.002 PHE A 34 TRP 0.007 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 3310) covalent geometry : angle 0.64446 / 0.31 ( 4583) hydrogen bonds : bond 0.04238 / 2.88 ( 244) hydrogen bonds : angle 3.82785 / 2.92 ( 732) *********************** 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 106 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.138 Fit side-chains REVERT: A 42 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8454 (mtm-85) REVERT: A 45 GLU cc_start: 0.8858 (tt0) cc_final: 0.8612 (tt0) REVERT: A 51 TYR cc_start: 0.8702 (t80) cc_final: 0.8125 (t80) REVERT: A 101 LEU cc_start: 0.8909 (mt) cc_final: 0.8660 (mp) REVERT: A 119 MET cc_start: 0.8687 (mmm) cc_final: 0.8446 (mmm) REVERT: A 195 PHE cc_start: 0.7239 (t80) cc_final: 0.6547 (t80) REVERT: A 268 ARG cc_start: 0.8012 (mtt90) cc_final: 0.7803 (mtt90) REVERT: A 300 ASN cc_start: 0.8258 (t0) cc_final: 0.8000 (t0) REVERT: A 336 LYS cc_start: 0.8335 (mttt) cc_final: 0.8067 (mmtm) REVERT: A 338 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 431 GLN cc_start: 0.8122 (tt0) cc_final: 0.7851 (mt0) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.0636 time to fit residues: 7.9790 Evaluate side-chains 100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3740 r_free = 0.3740 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125048 restraints weight = 5978.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128756 restraints weight = 3234.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131278 restraints weight = 1993.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133032 restraints weight = 1339.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134346 restraints weight = 947.343| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3310 Z= 0.141 Angle : 0.691 9.139 4583 Z= 0.326 Chirality : 0.039 0.205 585 Planarity : 0.004 0.041 518 Dihedral : 9.562 109.501 449 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.56 % Allowed : 21.50 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.43), residues: 393 helix: 2.69 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -0.95 (0.82), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.010 0.001 TYR A 35 PHE 0.015 0.001 PHE A 34 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 3310) covalent geometry : angle 0.69140 / 0.33 ( 4583) hydrogen bonds : bond 0.04339 / 2.93 ( 244) hydrogen bonds : angle 3.89352 / 2.95 ( 732) *********************** 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 108 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.114 Fit side-chains REVERT: A 51 TYR cc_start: 0.8679 (t80) cc_final: 0.8138 (t80) REVERT: A 59 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 101 LEU cc_start: 0.8895 (mt) cc_final: 0.8657 (mp) REVERT: A 119 MET cc_start: 0.8544 (mmm) cc_final: 0.8268 (mmm) REVERT: A 130 MET cc_start: 0.8546 (mtm) cc_final: 0.8302 (ptp) REVERT: A 133 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.7217 (mpt-90) REVERT: A 300 ASN cc_start: 0.8119 (t0) cc_final: 0.7918 (t0) REVERT: A 336 LYS cc_start: 0.8343 (mttt) cc_final: 0.8074 (mmtm) REVERT: A 338 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8050 (tt) REVERT: A 431 GLN cc_start: 0.8038 (tt0) cc_final: 0.7760 (mt0) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.0546 time to fit residues: 6.9010 Evaluate side-chains 102 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain A residue 63 GLN 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 284 VAL 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 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125887 restraints weight = 6069.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129678 restraints weight = 3268.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.132233 restraints weight = 1989.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134054 restraints weight = 1325.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135288 restraints weight = 923.652| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3310 Z= 0.139 Angle : 0.689 9.093 4583 Z= 0.326 Chirality : 0.039 0.182 585 Planarity : 0.004 0.041 518 Dihedral : 9.542 109.698 449 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.58 % Allowed : 23.13 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.43), residues: 393 helix: 2.65 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.02 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 42 TYR 0.010 0.001 TYR A 92 PHE 0.018 0.001 PHE A 34 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 3310) covalent geometry : angle 0.68947 / 0.33 ( 4583) hydrogen bonds : bond 0.04316 / 2.94 ( 244) hydrogen bonds : angle 3.90115 / 2.95 ( 732) *********************** 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 104 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.079 Fit side-chains REVERT: A 42 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: A 45 GLU cc_start: 0.8780 (tt0) cc_final: 0.8521 (tt0) REVERT: A 51 TYR cc_start: 0.8680 (t80) cc_final: 0.8108 (t80) REVERT: A 59 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: A 101 LEU cc_start: 0.8898 (mt) cc_final: 0.8666 (mp) REVERT: A 119 MET cc_start: 0.8528 (mmm) cc_final: 0.8222 (mmm) REVERT: A 133 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8203 (mpt-90) REVERT: A 134 ILE cc_start: 0.9192 (pt) cc_final: 0.8960 (mt) REVERT: A 300 ASN cc_start: 0.8112 (t0) cc_final: 0.7908 (t0) REVERT: A 336 LYS cc_start: 0.8338 (mttt) cc_final: 0.8072 (mmtm) REVERT: A 431 GLN cc_start: 0.8000 (tt0) cc_final: 0.7752 (mt0) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.0516 time to fit residues: 6.4187 Evaluate side-chains 95 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.111 ------------------------------------------------------------------------------- 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 284 VAL 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 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3738 r_free = 0.3738 target = 0.138578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125015 restraints weight = 5995.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128753 restraints weight = 3214.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131242 restraints weight = 1963.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133009 restraints weight = 1313.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134225 restraints weight = 926.453| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3310 Z= 0.142 Angle : 0.719 9.745 4583 Z= 0.337 Chirality : 0.039 0.192 585 Planarity : 0.004 0.041 518 Dihedral : 9.522 109.496 449 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 25.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.43), residues: 393 helix: 2.66 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -1.49 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.014 0.002 TYR A 92 PHE 0.020 0.001 PHE A 103 TRP 0.007 0.001 TRP A 270 HIS 0.002 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3310) covalent geometry : angle 0.71944 / 0.34 ( 4583) hydrogen bonds : bond 0.04343 / 2.95 ( 244) hydrogen bonds : angle 3.93653 / 2.98 ( 732) *********************** 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 99 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.139 Fit side-chains REVERT: A 51 TYR cc_start: 0.8648 (t80) cc_final: 0.8085 (t80) REVERT: A 101 LEU cc_start: 0.8856 (mt) cc_final: 0.8616 (mp) REVERT: A 119 MET cc_start: 0.8554 (mmm) cc_final: 0.8256 (mmm) REVERT: A 133 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8189 (mpt-90) REVERT: A 134 ILE cc_start: 0.9214 (pt) cc_final: 0.8990 (mt) REVERT: A 336 LYS cc_start: 0.8339 (mttt) cc_final: 0.8066 (mmtm) REVERT: A 431 GLN cc_start: 0.7983 (tt0) cc_final: 0.7749 (mt0) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.0599 time to fit residues: 7.0645 Evaluate side-chains 97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 284 VAL 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 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3773 r_free = 0.3773 target = 0.141281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127397 restraints weight = 5861.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131160 restraints weight = 3175.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133757 restraints weight = 1960.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135626 restraints weight = 1295.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136902 restraints weight = 898.282| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3310 Z= 0.130 Angle : 0.698 9.028 4583 Z= 0.328 Chirality : 0.038 0.197 585 Planarity : 0.004 0.042 518 Dihedral : 9.432 109.088 449 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.95 % Allowed : 26.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.43), residues: 393 helix: 2.62 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.24 (0.79), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.039 0.002 TYR A 366 PHE 0.018 0.001 PHE A 103 TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 3310) covalent geometry : angle 0.69840 / 0.33 ( 4583) hydrogen bonds : bond 0.04079 / 2.78 ( 244) hydrogen bonds : angle 3.84735 / 2.93 ( 732) ********************** 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 100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.110 Fit side-chains REVERT: A 42 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: A 45 GLU cc_start: 0.8753 (tt0) cc_final: 0.8469 (tt0) REVERT: A 51 TYR cc_start: 0.8601 (t80) cc_final: 0.8056 (t80) REVERT: A 101 LEU cc_start: 0.8837 (mt) cc_final: 0.8627 (mp) REVERT: A 122 MET cc_start: 0.7975 (ppp) cc_final: 0.7768 (ppp) REVERT: A 133 ARG cc_start: 0.8498 (mtt-85) cc_final: 0.8166 (mpt-90) REVERT: A 336 LYS cc_start: 0.8309 (mttt) cc_final: 0.8076 (mmtm) outliers start: 6 outliers final: 6 residues processed: 98 average time/residue: 0.0592 time to fit residues: 7.1280 Evaluate side-chains 98 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.067 ------------------------------------------------------------------------------- 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 284 VAL 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: 0.7980 chunk 18 optimal weight: 0.0030 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126165 restraints weight = 6041.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129862 restraints weight = 3271.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132361 restraints weight = 2019.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134234 restraints weight = 1362.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135485 restraints weight = 958.574| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4911 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= 0.133 Angle : 0.726 9.018 4583 Z= 0.339 Chirality : 0.038 0.189 585 Planarity : 0.004 0.041 518 Dihedral : 9.428 109.070 449 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.63 % Allowed : 28.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.43), residues: 393 helix: 2.61 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.25 (0.78), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.014 0.001 TYR A 92 PHE 0.019 0.001 PHE A 103 TRP 0.008 0.001 TRP A 270 HIS 0.001 0.000 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 3310) covalent geometry : angle 0.72602 / 0.34 ( 4583) hydrogen bonds : bond 0.04095 / 2.78 ( 244) hydrogen bonds : angle 3.82835 / 2.92 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 663.90 seconds wall clock time: 12 minutes 6.91 seconds (726.91 seconds total)