Starting phenix.real_space_refine on Tue Mar 3 11:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.map" model { file = "/net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tx6_26155/03_2026/7tx6_26155.cif" } resolution = 3.3 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 10 5.16 5 C 2122 2.51 5 N 503 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3169 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 1, 'MTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MTX:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 0.88, per 1000 atoms: 0.28 Number of scatterers: 3169 At special positions: 0 Unit cell: (72.36, 61.56, 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 10 16.00 O 534 8.00 N 503 7.00 C 2122 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 82.6 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A2644 " Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 4.105A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.835A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.986A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 3.861A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.562A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.906A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.538A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.616A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.936A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.511A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 326 removed outlier: 4.015A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 328 No H-bonds generated for 'chain 'A' and resid 327 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.097A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 334 " --> pdb=" O TRP A 331 " (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 389 removed outlier: 3.702A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.726A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 459 removed outlier: 3.664A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 714 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: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 446 1.31 - 1.43: 993 1.43 - 1.56: 1806 1.56 - 1.68: 5 1.68 - 1.81: 15 Bond restraints: 3265 Sorted by residual: bond pdb=" C VAL A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.449 -0.114 1.31e-02 5.83e+03 7.53e+01 bond pdb=" C4 MTX A2644 " pdb=" NA4 MTX A2644 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MTX A2644 " pdb=" C MTX A2644 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C2 MTX A2644 " pdb=" NA2 MTX A2644 " ideal model delta sigma weight residual 1.341 1.451 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C14 MTX A2644 " pdb=" N10 MTX A2644 " ideal model delta sigma weight residual 1.368 1.453 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4147 1.56 - 3.11: 237 3.11 - 4.67: 79 4.67 - 6.23: 13 6.23 - 7.79: 4 Bond angle restraints: 4480 Sorted by residual: angle pdb=" C VAL A 410 " pdb=" N LYS A 411 " pdb=" CA LYS A 411 " ideal model delta sigma weight residual 120.28 114.07 6.21 1.34e+00 5.57e-01 2.15e+01 angle pdb=" CA ILE A 48 " pdb=" C ILE A 48 " pdb=" O ILE A 48 " ideal model delta sigma weight residual 121.17 116.45 4.72 1.06e+00 8.90e-01 1.98e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 120.85 116.34 4.51 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.57 116.30 4.27 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N PHE A 416 " pdb=" CA PHE A 416 " pdb=" C PHE A 416 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 ... (remaining 4475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 1837 24.23 - 48.46: 81 48.46 - 72.69: 7 72.69 - 96.92: 8 96.92 - 121.14: 7 Dihedral angle restraints: 1940 sinusoidal: 769 harmonic: 1171 Sorted by residual: dihedral pdb=" C02 AJP A2501 " pdb=" C85 AJP A2501 " pdb=" O84 AJP A2501 " pdb=" C05 AJP A2501 " ideal model delta sinusoidal sigma weight residual -57.60 63.54 -121.14 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C28 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O31 AJP A2501 " ideal model delta sinusoidal sigma weight residual -54.31 65.16 -119.47 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O31 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O78 AJP A2501 " ideal model delta sinusoidal sigma weight residual 175.34 56.37 118.97 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 469 0.070 - 0.141: 50 0.141 - 0.211: 12 0.211 - 0.281: 6 0.281 - 0.352: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" C11 AJP A2501 " pdb=" C10 AJP A2501 " pdb=" C12 AJP A2501 " pdb=" C16 AJP A2501 " both_signs ideal model delta sigma weight residual False 2.20 2.56 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C15 AJP A2501 " pdb=" C14 AJP A2501 " pdb=" C16 AJP A2501 " pdb=" C20 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.42 -2.70 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C23 AJP A2501 " pdb=" C22 AJP A2501 " pdb=" C24 AJP A2501 " pdb=" O25 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 62 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLU A 62 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU A 62 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 63 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 94 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 68 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE A 68 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1092 2.84 - 3.36: 3421 3.36 - 3.87: 5070 3.87 - 4.39: 5536 4.39 - 4.90: 9405 Nonbonded interactions: 24524 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" N SER A 301 " model vdw 2.327 3.120 nonbonded pdb=" OD1 ASP A 56 " pdb=" N LYS A 57 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 102 " pdb=" OG SER A 105 " model vdw 2.421 3.040 nonbonded pdb=" O LEU A 440 " pdb=" OG SER A 443 " model vdw 2.482 3.040 nonbonded pdb=" O THR A 87 " pdb=" O LEU A 90 " model vdw 2.484 3.040 ... (remaining 24519 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 individual isotropic 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.230 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 0.121 3266 Z= 0.476 Angle : 0.902 7.786 4480 Z= 0.564 Chirality : 0.055 0.352 538 Planarity : 0.005 0.071 529 Dihedral : 17.014 121.145 1188 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 6.88 % Favored : 92.50 % Cbeta Deviations : 0.27 % 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: 2.51 (0.42), residues: 394 helix: 2.27 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.83 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.013 0.001 TYR A 438 PHE 0.010 0.001 PHE A 405 TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00798 ( 3265) covalent geometry : angle 0.90230 ( 4480) hydrogen bonds : bond 0.16694 ( 239) hydrogen bonds : angle 5.10258 ( 714) Misc. bond : bond 0.01909 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 282 TYR cc_start: 0.8320 (m-80) cc_final: 0.8030 (m-10) REVERT: A 287 TYR cc_start: 0.8373 (m-80) cc_final: 0.7723 (m-80) REVERT: A 363 TRP cc_start: 0.2795 (m100) cc_final: 0.2102 (m100) REVERT: A 395 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7789 (tt) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.0653 time to fit residues: 8.2360 Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130318 restraints weight = 5196.443| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.48 r_work: 0.3478 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3266 Z= 0.145 Angle : 0.658 7.541 4480 Z= 0.315 Chirality : 0.039 0.175 538 Planarity : 0.004 0.064 529 Dihedral : 9.137 74.081 571 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.88 % Allowed : 15.94 % Favored : 82.19 % Cbeta Deviations : 0.27 % 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: 3.21 (0.43), residues: 394 helix: 2.66 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.51 (0.81), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 268 TYR 0.013 0.001 TYR A 305 PHE 0.013 0.001 PHE A 432 TRP 0.012 0.001 TRP A 334 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3265) covalent geometry : angle 0.65847 ( 4480) hydrogen bonds : bond 0.04994 ( 239) hydrogen bonds : angle 3.64926 ( 714) Misc. bond : bond 0.00085 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 0.0573 time to fit residues: 6.5593 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134516 restraints weight = 5148.514| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.38 r_work: 0.3544 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3266 Z= 0.106 Angle : 0.558 7.823 4480 Z= 0.267 Chirality : 0.035 0.120 538 Planarity : 0.004 0.060 529 Dihedral : 6.990 75.619 569 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.25 % Allowed : 21.25 % Favored : 77.50 % Cbeta Deviations : 0.27 % 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: 3.40 (0.43), residues: 394 helix: 2.91 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -0.91 (0.78), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 373 TYR 0.009 0.001 TYR A 438 PHE 0.012 0.001 PHE A 34 TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3265) covalent geometry : angle 0.55791 ( 4480) hydrogen bonds : bond 0.03933 ( 239) hydrogen bonds : angle 3.27623 ( 714) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9080 (m) cc_final: 0.8553 (p) outliers start: 4 outliers final: 3 residues processed: 91 average time/residue: 0.0648 time to fit residues: 7.2534 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.126250 restraints weight = 5207.398| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.38 r_work: 0.3440 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3266 Z= 0.197 Angle : 0.617 7.041 4480 Z= 0.316 Chirality : 0.038 0.119 538 Planarity : 0.004 0.057 529 Dihedral : 7.183 84.003 569 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.50 % Allowed : 23.75 % Favored : 73.75 % Cbeta Deviations : 0.27 % 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: 3.03 (0.43), residues: 394 helix: 2.61 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.65 (0.77), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 373 TYR 0.011 0.001 TYR A 35 PHE 0.010 0.001 PHE A 165 TRP 0.017 0.001 TRP A 334 HIS 0.005 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3265) covalent geometry : angle 0.61691 ( 4480) hydrogen bonds : bond 0.05358 ( 239) hydrogen bonds : angle 3.62275 ( 714) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8421 (tt0) REVERT: A 133 ARG cc_start: 0.8530 (ttp-170) cc_final: 0.7986 (ptt180) outliers start: 8 outliers final: 7 residues processed: 90 average time/residue: 0.0654 time to fit residues: 7.1655 Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129507 restraints weight = 5191.011| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.48 r_work: 0.3479 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3266 Z= 0.120 Angle : 0.575 9.277 4480 Z= 0.279 Chirality : 0.036 0.120 538 Planarity : 0.004 0.057 529 Dihedral : 7.120 82.544 569 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.25 % Allowed : 25.31 % Favored : 73.44 % Cbeta Deviations : 0.27 % 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: 3.28 (0.43), residues: 394 helix: 2.71 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.53 (0.81), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.009 0.001 TYR A 438 PHE 0.010 0.001 PHE A 165 TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3265) covalent geometry : angle 0.57454 ( 4480) hydrogen bonds : bond 0.04371 ( 239) hydrogen bonds : angle 3.35510 ( 714) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8062 (tt0) REVERT: A 102 SER cc_start: 0.9089 (m) cc_final: 0.8585 (p) REVERT: A 119 MET cc_start: 0.8576 (mmm) cc_final: 0.8259 (mmm) REVERT: A 133 ARG cc_start: 0.8545 (ttp-170) cc_final: 0.8337 (ttp-170) REVERT: A 394 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8542 (tm-30) outliers start: 4 outliers final: 2 residues processed: 93 average time/residue: 0.0601 time to fit residues: 6.8827 Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128842 restraints weight = 5111.603| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.37 r_work: 0.3473 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3266 Z= 0.137 Angle : 0.593 8.917 4480 Z= 0.288 Chirality : 0.036 0.115 538 Planarity : 0.004 0.056 529 Dihedral : 7.099 80.575 569 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.25 % Allowed : 25.94 % Favored : 72.81 % Cbeta Deviations : 0.27 % 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: 3.24 (0.43), residues: 394 helix: 2.77 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.64 (0.77), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 373 TYR 0.010 0.001 TYR A 35 PHE 0.010 0.001 PHE A 34 TRP 0.011 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 3265) covalent geometry : angle 0.59287 ( 4480) hydrogen bonds : bond 0.04529 ( 239) hydrogen bonds : angle 3.37363 ( 714) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.6662 (mmtp) cc_final: 0.6282 (mmtp) REVERT: A 99 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8069 (tt0) REVERT: A 102 SER cc_start: 0.9106 (m) cc_final: 0.8592 (p) REVERT: A 394 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8511 (tm-30) outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 0.0726 time to fit residues: 8.0892 Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129467 restraints weight = 5230.943| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.43 r_work: 0.3477 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3266 Z= 0.132 Angle : 0.603 10.606 4480 Z= 0.289 Chirality : 0.036 0.129 538 Planarity : 0.004 0.055 529 Dihedral : 7.249 82.196 569 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.94 % Allowed : 26.56 % Favored : 72.50 % Cbeta Deviations : 0.27 % 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: 3.26 (0.43), residues: 394 helix: 2.78 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -0.65 (0.77), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 373 TYR 0.010 0.001 TYR A 35 PHE 0.009 0.001 PHE A 165 TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3265) covalent geometry : angle 0.60313 ( 4480) hydrogen bonds : bond 0.04390 ( 239) hydrogen bonds : angle 3.34659 ( 714) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.6787 (mmtp) cc_final: 0.6403 (mmtp) REVERT: A 99 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8050 (tt0) REVERT: A 102 SER cc_start: 0.9097 (m) cc_final: 0.8585 (p) REVERT: A 133 ARG cc_start: 0.8562 (ttp-170) cc_final: 0.8136 (ptt180) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.0628 time to fit residues: 6.9039 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128223 restraints weight = 5314.185| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.45 r_work: 0.3464 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3266 Z= 0.139 Angle : 0.628 10.963 4480 Z= 0.297 Chirality : 0.036 0.137 538 Planarity : 0.004 0.055 529 Dihedral : 7.274 82.399 569 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.94 % Allowed : 26.88 % Favored : 72.19 % Cbeta Deviations : 0.27 % 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: 3.23 (0.42), residues: 394 helix: 2.79 (0.28), residues: 316 sheet: None (None), residues: 0 loop : -0.80 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.010 0.001 TYR A 35 PHE 0.011 0.001 PHE A 34 TRP 0.011 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3265) covalent geometry : angle 0.62829 ( 4480) hydrogen bonds : bond 0.04513 ( 239) hydrogen bonds : angle 3.39023 ( 714) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8072 (tt0) REVERT: A 102 SER cc_start: 0.9094 (m) cc_final: 0.8579 (p) outliers start: 3 outliers final: 2 residues processed: 88 average time/residue: 0.0614 time to fit residues: 6.6377 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.0170 chunk 30 optimal weight: 0.2980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.133982 restraints weight = 5220.980| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.51 r_work: 0.3554 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3266 Z= 0.104 Angle : 0.618 12.231 4480 Z= 0.282 Chirality : 0.034 0.142 538 Planarity : 0.004 0.055 529 Dihedral : 7.110 81.779 569 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.94 % Allowed : 26.88 % Favored : 72.19 % Cbeta Deviations : 0.27 % 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: 3.44 (0.42), residues: 394 helix: 2.96 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -1.03 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.007 0.001 TYR A 376 PHE 0.009 0.001 PHE A 165 TRP 0.011 0.001 TRP A 270 HIS 0.001 0.000 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 3265) covalent geometry : angle 0.61782 ( 4480) hydrogen bonds : bond 0.03625 ( 239) hydrogen bonds : angle 3.19670 ( 714) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.107 Fit side-chains REVERT: A 99 GLN cc_start: 0.8737 (tm-30) cc_final: 0.7991 (tt0) REVERT: A 102 SER cc_start: 0.8980 (m) cc_final: 0.8615 (p) REVERT: A 133 ARG cc_start: 0.8538 (ttp-170) cc_final: 0.8017 (ptt180) outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.0646 time to fit residues: 7.0291 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.143567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132239 restraints weight = 5243.196| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.51 r_work: 0.3532 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3266 Z= 0.117 Angle : 0.665 13.172 4480 Z= 0.299 Chirality : 0.035 0.146 538 Planarity : 0.004 0.054 529 Dihedral : 7.264 86.281 569 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.25 % Allowed : 26.25 % Favored : 72.50 % Cbeta Deviations : 0.27 % 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 (0.42), residues: 394 helix: 2.92 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -1.10 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.008 0.001 TYR A 35 PHE 0.013 0.001 PHE A 34 TRP 0.009 0.001 TRP A 270 HIS 0.002 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3265) covalent geometry : angle 0.66541 ( 4480) hydrogen bonds : bond 0.03951 ( 239) hydrogen bonds : angle 3.24025 ( 714) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.109 Fit side-chains REVERT: A 102 SER cc_start: 0.9034 (m) cc_final: 0.8807 (p) REVERT: A 133 ARG cc_start: 0.8588 (ttp-170) cc_final: 0.8061 (ptt180) outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.0684 time to fit residues: 7.1141 Evaluate side-chains 85 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.0030 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132257 restraints weight = 5223.130| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.51 r_work: 0.3531 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3266 Z= 0.117 Angle : 0.668 12.929 4480 Z= 0.298 Chirality : 0.036 0.151 538 Planarity : 0.004 0.054 529 Dihedral : 7.271 87.668 569 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.62 % Allowed : 27.50 % Favored : 71.88 % Cbeta Deviations : 0.27 % 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: 3.40 (0.42), residues: 394 helix: 2.92 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.01 (0.72), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.008 0.001 TYR A 35 PHE 0.009 0.001 PHE A 165 TRP 0.009 0.001 TRP A 270 HIS 0.002 0.000 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3265) covalent geometry : angle 0.66782 ( 4480) hydrogen bonds : bond 0.03923 ( 239) hydrogen bonds : angle 3.18715 ( 714) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 839.20 seconds wall clock time: 15 minutes 1.20 seconds (901.20 seconds total)