Starting phenix.real_space_refine on Wed Mar 5 21:03:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_26156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_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/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_26156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_26156.map" model { file = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_26156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2025/7tx7_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-5624/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: 2.60, per 1000 atoms: 0.81 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: 0.86 Conformation dependent library (CDL) restraints added in 357.7 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: 0.25 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: 0.77 Time building geometry restraints manager: 1.00 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.341 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: 0.1645 time to fit residues: 25.4787 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 : 0.347 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126377 restraints weight = 5978.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130190 restraints weight = 3218.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132699 restraints weight = 1963.269| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.312 Fit side-chains REVERT: A 51 TYR cc_start: 0.8789 (t80) cc_final: 0.8089 (t80) REVERT: A 133 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7615 (mtt90) REVERT: A 195 PHE cc_start: 0.7390 (t80) cc_final: 0.6564 (t80) REVERT: A 300 ASN cc_start: 0.8374 (t0) cc_final: 0.8082 (t0) outliers start: 6 outliers final: 6 residues processed: 113 average time/residue: 0.1248 time to fit residues: 17.5351 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 : 0.312 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.137745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124072 restraints weight = 5928.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127414 restraints weight = 3206.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130123 restraints weight = 2046.443| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.211 Angle : 0.635 6.756 4583 Z= 0.304 Chirality : 0.037 0.134 585 Planarity : 0.004 0.048 518 Dihedral : 10.308 129.100 891 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.93 % Allowed : 19.87 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.43), residues: 393 helix: 3.02 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.33 (0.82), residues: 69 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 0.013 0.001 PHE A 103 TYR 0.015 0.002 TYR A 35 ARG 0.004 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.334 Fit side-chains REVERT: A 32 LEU cc_start: 0.8662 (mp) cc_final: 0.8461 (tp) REVERT: A 51 TYR cc_start: 0.8752 (t80) cc_final: 0.7988 (t80) REVERT: A 133 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7606 (mtt90) REVERT: A 195 PHE cc_start: 0.7200 (t80) cc_final: 0.6416 (t80) REVERT: A 300 ASN cc_start: 0.8320 (t0) cc_final: 0.7924 (t0) REVERT: A 336 LYS cc_start: 0.8397 (mttt) cc_final: 0.8077 (mmtm) outliers start: 9 outliers final: 8 residues processed: 103 average time/residue: 0.1266 time to fit residues: 16.2892 Evaluate side-chains 97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124285 restraints weight = 5986.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128031 restraints weight = 3232.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130579 restraints weight = 1971.888| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3593 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= 0.181 Angle : 0.605 8.290 4583 Z= 0.291 Chirality : 0.035 0.114 585 Planarity : 0.004 0.045 518 Dihedral : 9.346 118.493 891 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.91 % Allowed : 18.89 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.43), residues: 393 helix: 2.92 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -0.76 (0.82), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.014 0.001 PHE A 326 TYR 0.019 0.002 TYR A 366 ARG 0.003 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8935 (tt0) cc_final: 0.8662 (tt0) REVERT: A 51 TYR cc_start: 0.8704 (t80) cc_final: 0.8009 (t80) REVERT: A 195 PHE cc_start: 0.7207 (t80) cc_final: 0.6403 (t80) REVERT: A 300 ASN cc_start: 0.8291 (t0) cc_final: 0.7964 (t0) REVERT: A 336 LYS cc_start: 0.8345 (mttt) cc_final: 0.8079 (mmtm) REVERT: A 411 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7714 (ttmt) outliers start: 12 outliers final: 9 residues processed: 108 average time/residue: 0.1271 time to fit residues: 17.3590 Evaluate side-chains 97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 194 THR 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 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.127013 restraints weight = 5884.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130898 restraints weight = 3151.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133501 restraints weight = 1904.025| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3310 Z= 0.182 Angle : 0.634 8.106 4583 Z= 0.306 Chirality : 0.037 0.194 585 Planarity : 0.004 0.043 518 Dihedral : 7.590 81.719 891 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.58 % Allowed : 20.52 % Favored : 75.90 % 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: 3.48 (0.44), residues: 393 helix: 2.76 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.55 (0.86), residues: 60 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 0.028 0.002 PHE A 34 TYR 0.025 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 to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.306 Fit side-chains REVERT: A 51 TYR cc_start: 0.8671 (t80) cc_final: 0.8047 (t80) REVERT: A 101 LEU cc_start: 0.8915 (mt) cc_final: 0.8674 (mp) REVERT: A 195 PHE cc_start: 0.7237 (t80) cc_final: 0.6470 (t80) REVERT: A 300 ASN cc_start: 0.8318 (t0) cc_final: 0.8052 (t0) REVERT: A 336 LYS cc_start: 0.8313 (mttt) cc_final: 0.8070 (mmtm) REVERT: A 338 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (tt) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1225 time to fit residues: 16.4364 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 : 0.304 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 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 = 0.3740 r_free = 0.3740 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125126 restraints weight = 6024.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129016 restraints weight = 3269.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131535 restraints weight = 1990.820| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3310 Z= 0.195 Angle : 0.664 9.688 4583 Z= 0.317 Chirality : 0.038 0.193 585 Planarity : 0.004 0.041 518 Dihedral : 5.651 52.351 891 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.58 % Allowed : 24.10 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.43), residues: 393 helix: 2.67 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.97 (0.82), residues: 61 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 0.016 0.001 PHE A 326 TYR 0.012 0.001 TYR A 35 ARG 0.004 0.000 ARG A 61 *********************** 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 99 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.351 Fit side-chains REVERT: A 51 TYR cc_start: 0.8671 (t80) cc_final: 0.8183 (t80) REVERT: A 133 ARG cc_start: 0.8547 (mtt-85) cc_final: 0.8215 (mtt90) REVERT: A 134 ILE cc_start: 0.9151 (pt) cc_final: 0.8942 (mt) REVERT: A 195 PHE cc_start: 0.7366 (t80) cc_final: 0.6720 (t80) REVERT: A 300 ASN cc_start: 0.8214 (t0) cc_final: 0.7963 (t0) REVERT: A 336 LYS cc_start: 0.8330 (mttt) cc_final: 0.8091 (mmtm) REVERT: A 338 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8059 (tt) outliers start: 11 outliers final: 8 residues processed: 95 average time/residue: 0.1281 time to fit residues: 15.2857 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 : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124596 restraints weight = 5845.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128387 restraints weight = 3161.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.130869 restraints weight = 1934.650| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3310 Z= 0.208 Angle : 0.668 9.098 4583 Z= 0.323 Chirality : 0.038 0.182 585 Planarity : 0.004 0.041 518 Dihedral : 5.539 51.770 891 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.58 % Allowed : 23.78 % 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: 3.15 (0.43), residues: 393 helix: 2.62 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.17 (0.81), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.002 0.001 HIS A 355 PHE 0.024 0.001 PHE A 103 TYR 0.009 0.001 TYR A 35 ARG 0.002 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 103 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8671 (t80) cc_final: 0.8201 (t80) REVERT: A 59 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: A 97 LEU cc_start: 0.8657 (tp) cc_final: 0.8363 (tp) REVERT: A 119 MET cc_start: 0.8675 (mmm) cc_final: 0.8314 (mmm) REVERT: A 195 PHE cc_start: 0.7421 (t80) cc_final: 0.6689 (t80) REVERT: A 300 ASN cc_start: 0.8248 (t0) cc_final: 0.8015 (t0) REVERT: A 336 LYS cc_start: 0.8334 (mttt) cc_final: 0.8096 (mmtm) REVERT: A 338 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8077 (tt) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.1311 time to fit residues: 16.3554 Evaluate side-chains 98 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126761 restraints weight = 5887.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130508 restraints weight = 3202.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133012 restraints weight = 1970.808| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3310 Z= 0.188 Angle : 0.697 14.187 4583 Z= 0.329 Chirality : 0.039 0.189 585 Planarity : 0.004 0.040 518 Dihedral : 5.310 52.086 891 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.58 % Allowed : 24.76 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.43), residues: 393 helix: 2.51 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.20 (0.79), 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 0.018 0.001 PHE A 103 TYR 0.035 0.002 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 102 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8640 (t80) cc_final: 0.8169 (t80) REVERT: A 59 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: A 133 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8244 (mtt90) REVERT: A 172 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7215 (tp40) REVERT: A 336 LYS cc_start: 0.8246 (mttt) cc_final: 0.7962 (mmtm) REVERT: A 338 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8046 (tt) outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1442 time to fit residues: 17.2547 Evaluate side-chains 96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 172 GLN 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 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126428 restraints weight = 5957.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130148 restraints weight = 3240.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132627 restraints weight = 1990.507| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.201 Angle : 0.734 16.623 4583 Z= 0.343 Chirality : 0.038 0.191 585 Planarity : 0.004 0.039 518 Dihedral : 5.296 51.365 891 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.58 % Allowed : 26.38 % Favored : 70.03 % 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: 3.02 (0.43), residues: 393 helix: 2.47 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.13 (0.84), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.002 0.001 HIS A 355 PHE 0.030 0.001 PHE A 34 TYR 0.038 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 to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8649 (t80) cc_final: 0.8170 (t80) REVERT: A 133 ARG cc_start: 0.8524 (mtt-85) cc_final: 0.8239 (mtt90) REVERT: A 172 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7241 (tp40) REVERT: A 336 LYS cc_start: 0.8331 (mttt) cc_final: 0.8099 (mmtm) REVERT: A 338 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8038 (tt) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.1476 time to fit residues: 17.4259 Evaluate side-chains 96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 172 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127316 restraints weight = 5836.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131037 restraints weight = 3176.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.133519 restraints weight = 1949.307| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.190 Angle : 0.731 16.624 4583 Z= 0.344 Chirality : 0.038 0.194 585 Planarity : 0.004 0.038 518 Dihedral : 5.208 51.184 891 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 27.04 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.43), residues: 393 helix: 2.41 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -0.93 (0.83), residues: 55 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 0.028 0.001 PHE A 34 TYR 0.015 0.001 TYR A 286 ARG 0.003 0.000 ARG A 61 ********************** 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 101 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.8614 (t80) cc_final: 0.8156 (t80) REVERT: A 133 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8207 (mtt90) REVERT: A 172 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7268 (tp40) REVERT: A 300 ASN cc_start: 0.8093 (t0) cc_final: 0.6992 (m-40) REVERT: A 336 LYS cc_start: 0.8284 (mttt) cc_final: 0.8000 (mmtm) REVERT: A 338 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8013 (tt) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 0.1513 time to fit residues: 18.0232 Evaluate side-chains 96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.140557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126808 restraints weight = 5905.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130546 restraints weight = 3222.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133001 restraints weight = 1984.569| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.195 Angle : 0.728 16.160 4583 Z= 0.342 Chirality : 0.038 0.190 585 Planarity : 0.004 0.038 518 Dihedral : 5.173 50.576 891 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.93 % Allowed : 27.36 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.43), residues: 393 helix: 2.45 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -0.91 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 270 HIS 0.001 0.001 HIS A 355 PHE 0.028 0.001 PHE A 34 TYR 0.040 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: 1265.09 seconds wall clock time: 22 minutes 32.81 seconds (1352.81 seconds total)