Starting phenix.real_space_refine on Wed Jul 1 22:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dep_27394/07_2026/8dep_27394.map" } resolution = 3.6 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= 0.034 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 2175 2.51 5 N 489 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3223 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3062 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 161 Unusual residues: {'AJP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 81 Time building chain proxies: 0.93, per 1000 atoms: 0.29 Number of scatterers: 3223 At special positions: 0 Unit cell: (74.52, 69.12, 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 552 8.00 N 489 7.00 C 2175 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: 0.30 Conformation dependent library (CDL) restraints added in 129.5 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 4.147A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.749A 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: 4.010A pdb=" N VAL A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.801A 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: 4.063A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.620A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.681A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 179 removed outlier: 3.922A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 203 removed outlier: 3.616A pdb=" N ALA A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.714A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 296 removed outlier: 4.090A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 327 removed outlier: 3.680A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.548A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) 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: 3.710A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 4.683A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.965A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 459 removed outlier: 3.561A pdb=" N VAL A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 238 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: 0.31 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 911 1.35 - 1.46: 916 1.46 - 1.58: 1491 1.58 - 1.69: 4 1.69 - 1.81: 11 Bond restraints: 3333 Sorted by residual: bond pdb=" C23 AJP A 703 " pdb=" C24 AJP A 703 " ideal model delta sigma weight residual 1.522 1.610 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C23 AJP A 702 " pdb=" C24 AJP A 702 " ideal model delta sigma weight residual 1.522 1.609 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C05 AJP A 704 " pdb=" C06 AJP A 704 " ideal model delta sigma weight residual 1.534 1.449 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 701 " pdb=" C24 AJP A 701 " ideal model delta sigma weight residual 1.522 1.607 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 AJP A 704 " pdb=" C24 AJP A 704 " ideal model delta sigma weight residual 1.522 1.606 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 3328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 4364 1.38 - 2.75: 155 2.75 - 4.13: 64 4.13 - 5.51: 26 5.51 - 6.88: 6 Bond angle restraints: 4615 Sorted by residual: angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 111.02 114.67 -3.65 1.22e+00 6.72e-01 8.95e+00 angle pdb=" N ILE A 41 " pdb=" CA ILE A 41 " pdb=" C ILE A 41 " ideal model delta sigma weight residual 106.55 110.75 -4.20 1.45e+00 4.76e-01 8.40e+00 angle pdb=" C ILE A 41 " pdb=" CA ILE A 41 " pdb=" CB ILE A 41 " ideal model delta sigma weight residual 112.68 109.72 2.96 1.14e+00 7.69e-01 6.74e+00 angle pdb=" C07 AJP A 701 " pdb=" C06 AJP A 701 " pdb=" C83 AJP A 701 " ideal model delta sigma weight residual 114.76 107.88 6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" N PHE A 202 " pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 111.82 114.30 -2.48 1.16e+00 7.43e-01 4.59e+00 ... (remaining 4610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.05: 1727 24.05 - 48.10: 62 48.10 - 72.15: 5 72.15 - 96.20: 1 96.20 - 120.25: 3 Dihedral angle restraints: 1798 sinusoidal: 627 harmonic: 1171 Sorted by residual: dihedral pdb=" C02 AJP A 703 " pdb=" C85 AJP A 703 " pdb=" O84 AJP A 703 " pdb=" C05 AJP A 703 " ideal model delta sinusoidal sigma weight residual -57.60 62.65 -120.25 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C02 AJP A 701 " pdb=" C85 AJP A 701 " pdb=" O84 AJP A 701 " pdb=" C05 AJP A 701 " ideal model delta sinusoidal sigma weight residual -57.60 62.51 -120.11 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C02 AJP A 704 " pdb=" C85 AJP A 704 " pdb=" O84 AJP A 704 " pdb=" C05 AJP A 704 " ideal model delta sinusoidal sigma weight residual -57.60 55.08 -112.68 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 1795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 512 0.070 - 0.140: 39 0.140 - 0.210: 15 0.210 - 0.280: 11 0.280 - 0.350: 9 Chirality restraints: 586 Sorted by residual: 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 2.55 -0.35 2.00e-01 2.50e+01 3.06e+00 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 2.73 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C23 AJP A 703 " pdb=" C22 AJP A 703 " pdb=" C24 AJP A 703 " pdb=" O25 AJP A 703 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 583 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 94 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 82 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 43 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.021 5.00e-02 4.00e+02 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 287 2.74 - 3.28: 3597 3.28 - 3.82: 5361 3.82 - 4.36: 5566 4.36 - 4.90: 9822 Nonbonded interactions: 24633 Sorted by model distance: nonbonded pdb=" O ALA A 135 " pdb=" OG SER A 138 " model vdw 2.197 3.040 nonbonded pdb=" O33 AJP A 701 " pdb=" O77 AJP A 701 " model vdw 2.221 3.040 nonbonded pdb=" O LEU A 124 " pdb=" OG SER A 127 " model vdw 2.350 3.040 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.410 3.040 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.424 3.040 ... (remaining 24628 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: 0.760 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.590 Find NCS groups from input model: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 0.088 3333 Z= 0.401 Angle : 0.764 6.883 4615 Z= 0.347 Chirality : 0.067 0.350 586 Planarity : 0.005 0.065 521 Dihedral : 13.588 120.247 1046 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 0.65 % Allowed : 8.09 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.41), residues: 394 helix: 2.57 (0.27), residues: 317 sheet: None (None), residues: 0 loop : -0.49 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 268 TYR 0.009 0.001 TYR A 35 PHE 0.008 0.001 PHE A 326 TRP 0.009 0.001 TRP A 107 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.40 ( 3333) covalent geometry : angle 0.76372 / 0.35 ( 4615) hydrogen bonds : bond 0.15026 / 9.18 ( 238) hydrogen bonds : angle 5.61415 / 4.25 ( 714) *********************** 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 120 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.107 Fit side-chains REVERT: A 45 GLU cc_start: 0.8175 (tt0) cc_final: 0.7965 (tt0) REVERT: A 75 SER cc_start: 0.9174 (m) cc_final: 0.8962 (t) REVERT: A 287 TYR cc_start: 0.8051 (m-80) cc_final: 0.7787 (m-10) REVERT: A 293 ASN cc_start: 0.8596 (t0) cc_final: 0.8340 (t0) REVERT: A 294 GLU cc_start: 0.7821 (tp30) cc_final: 0.7325 (tp30) REVERT: A 306 ASN cc_start: 0.8570 (m-40) cc_final: 0.8218 (t0) REVERT: A 310 ASP cc_start: 0.9019 (t0) cc_final: 0.8749 (t70) REVERT: A 316 LEU cc_start: 0.8900 (tp) cc_final: 0.8699 (tt) REVERT: A 346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8370 (mt0) REVERT: A 361 SER cc_start: 0.8810 (m) cc_final: 0.8588 (t) REVERT: A 412 THR cc_start: 0.8790 (m) cc_final: 0.8457 (m) outliers start: 2 outliers final: 0 residues processed: 119 average time/residue: 0.0450 time to fit residues: 6.8457 Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.109112 restraints weight = 5630.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112716 restraints weight = 2412.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114971 restraints weight = 1326.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116400 restraints weight = 863.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117484 restraints weight = 637.175| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3333 Z= 0.146 Angle : 0.650 7.152 4615 Z= 0.303 Chirality : 0.037 0.156 586 Planarity : 0.004 0.052 521 Dihedral : 9.293 108.670 450 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.24 % Allowed : 19.42 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.65 (0.42), residues: 394 helix: 2.87 (0.27), residues: 327 sheet: None (None), residues: 0 loop : -0.04 (0.87), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.016 0.002 TYR A 149 PHE 0.023 0.001 PHE A 141 TRP 0.012 0.001 TRP A 363 HIS 0.008 0.002 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 3333) covalent geometry : angle 0.64965 / 0.30 ( 4615) hydrogen bonds : bond 0.05465 / 3.53 ( 238) hydrogen bonds : angle 4.23152 / 3.19 ( 714) *********************** 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 112 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.104 Fit side-chains REVERT: A 45 GLU cc_start: 0.8259 (tt0) cc_final: 0.8021 (tt0) REVERT: A 75 SER cc_start: 0.9102 (m) cc_final: 0.8883 (t) REVERT: A 123 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8060 (mm-30) REVERT: A 172 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 181 SER cc_start: 0.8854 (m) cc_final: 0.8265 (p) REVERT: A 293 ASN cc_start: 0.8528 (t0) cc_final: 0.8096 (t0) REVERT: A 306 ASN cc_start: 0.8344 (m-40) cc_final: 0.7781 (t0) REVERT: A 310 ASP cc_start: 0.9016 (t0) cc_final: 0.8785 (t70) REVERT: A 346 GLN cc_start: 0.8705 (mt0) cc_final: 0.8166 (mt0) REVERT: A 361 SER cc_start: 0.8807 (m) cc_final: 0.8434 (t) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.0529 time to fit residues: 6.9897 Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 23 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 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 = 0.3474 r_free = 0.3474 target = 0.122869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108638 restraints weight = 5672.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112238 restraints weight = 2407.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114652 restraints weight = 1328.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116255 restraints weight = 848.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117260 restraints weight = 606.686| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3333 Z= 0.129 Angle : 0.610 7.991 4615 Z= 0.283 Chirality : 0.035 0.130 586 Planarity : 0.004 0.046 521 Dihedral : 9.430 110.570 450 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.24 % Allowed : 24.60 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.43), residues: 394 helix: 2.93 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.11 (0.84), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 133 TYR 0.020 0.002 TYR A 287 PHE 0.017 0.001 PHE A 141 TRP 0.009 0.001 TRP A 107 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 3333) covalent geometry : angle 0.60995 / 0.28 ( 4615) hydrogen bonds : bond 0.04546 / 2.93 ( 238) hydrogen bonds : angle 3.82811 / 2.88 ( 714) *********************** 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 103 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.116 Fit side-chains REVERT: A 45 GLU cc_start: 0.8322 (tt0) cc_final: 0.8060 (tt0) REVERT: A 119 MET cc_start: 0.8983 (mmm) cc_final: 0.8781 (mmp) REVERT: A 123 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 172 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 181 SER cc_start: 0.8806 (m) cc_final: 0.8237 (p) REVERT: A 277 ASN cc_start: 0.8761 (m-40) cc_final: 0.8485 (m-40) REVERT: A 293 ASN cc_start: 0.8443 (t0) cc_final: 0.8202 (t0) REVERT: A 306 ASN cc_start: 0.8384 (m-40) cc_final: 0.7773 (t0) REVERT: A 310 ASP cc_start: 0.9124 (t0) cc_final: 0.8840 (t70) REVERT: A 346 GLN cc_start: 0.8632 (mt0) cc_final: 0.8138 (mt0) REVERT: A 393 LYS cc_start: 0.8607 (tppt) cc_final: 0.8293 (tptp) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.0391 time to fit residues: 5.0392 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103963 restraints weight = 5707.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107435 restraints weight = 2451.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109773 restraints weight = 1349.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111169 restraints weight = 866.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112218 restraints weight = 632.493| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3333 Z= 0.169 Angle : 0.629 6.908 4615 Z= 0.293 Chirality : 0.036 0.119 586 Planarity : 0.004 0.044 521 Dihedral : 9.213 109.935 450 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.50 % Allowed : 25.89 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.43), residues: 394 helix: 2.70 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.41 (0.81), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.020 0.002 TYR A 366 PHE 0.010 0.001 PHE A 141 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 ( 3333) covalent geometry : angle 0.62941 / 0.29 ( 4615) hydrogen bonds : bond 0.04716 / 3.09 ( 238) hydrogen bonds : angle 3.96885 / 2.99 ( 714) *********************** 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 108 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.101 Fit side-chains REVERT: A 45 GLU cc_start: 0.8369 (tt0) cc_final: 0.8100 (tt0) REVERT: A 123 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 181 SER cc_start: 0.8903 (m) cc_final: 0.8341 (p) REVERT: A 277 ASN cc_start: 0.8754 (m-40) cc_final: 0.8442 (m-40) REVERT: A 287 TYR cc_start: 0.7988 (m-10) cc_final: 0.7756 (m-10) REVERT: A 293 ASN cc_start: 0.8421 (t0) cc_final: 0.7898 (t0) REVERT: A 294 GLU cc_start: 0.7879 (tp30) cc_final: 0.7160 (tp30) REVERT: A 306 ASN cc_start: 0.8404 (m-40) cc_final: 0.7796 (t0) REVERT: A 310 ASP cc_start: 0.9169 (t0) cc_final: 0.8843 (t0) REVERT: A 346 GLN cc_start: 0.8693 (mt0) cc_final: 0.8188 (mt0) REVERT: A 393 LYS cc_start: 0.8746 (tppt) cc_final: 0.8434 (tptp) REVERT: A 412 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8742 (t) outliers start: 17 outliers final: 9 residues processed: 102 average time/residue: 0.0468 time to fit residues: 6.1453 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.3400 r_free = 0.3400 target = 0.117762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104117 restraints weight = 5722.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107555 restraints weight = 2443.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109831 restraints weight = 1350.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111208 restraints weight = 868.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112248 restraints weight = 636.381| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3333 Z= 0.164 Angle : 0.651 9.343 4615 Z= 0.300 Chirality : 0.037 0.168 586 Planarity : 0.004 0.044 521 Dihedral : 9.288 110.438 450 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.21 % Allowed : 27.83 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.42), residues: 394 helix: 2.59 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.54 (0.79), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.028 0.002 TYR A 366 PHE 0.010 0.001 PHE A 59 TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 3333) covalent geometry : angle 0.65074 / 0.30 ( 4615) hydrogen bonds : bond 0.04595 / 3.00 ( 238) hydrogen bonds : angle 3.96330 / 3.01 ( 714) *********************** 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 97 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.106 Fit side-chains REVERT: A 45 GLU cc_start: 0.8365 (tt0) cc_final: 0.8095 (tt0) REVERT: A 123 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 277 ASN cc_start: 0.8744 (m-40) cc_final: 0.8483 (m110) REVERT: A 287 TYR cc_start: 0.7977 (m-10) cc_final: 0.7622 (m-10) REVERT: A 293 ASN cc_start: 0.8436 (t0) cc_final: 0.7936 (t0) REVERT: A 294 GLU cc_start: 0.7938 (tp30) cc_final: 0.7191 (tp30) REVERT: A 306 ASN cc_start: 0.8510 (m-40) cc_final: 0.7886 (t0) REVERT: A 310 ASP cc_start: 0.9140 (t0) cc_final: 0.8835 (t0) REVERT: A 313 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9057 (p) REVERT: A 346 GLN cc_start: 0.8721 (mt0) cc_final: 0.8229 (mt0) REVERT: A 412 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8768 (t) outliers start: 13 outliers final: 8 residues processed: 90 average time/residue: 0.0388 time to fit residues: 4.5091 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106669 restraints weight = 5674.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.110181 restraints weight = 2408.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112464 restraints weight = 1321.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113963 restraints weight = 854.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115054 restraints weight = 616.891| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3333 Z= 0.130 Angle : 0.613 7.899 4615 Z= 0.282 Chirality : 0.035 0.111 586 Planarity : 0.004 0.043 521 Dihedral : 9.252 110.154 450 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.24 % Allowed : 29.13 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.57 (0.78), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.028 0.002 TYR A 149 PHE 0.007 0.001 PHE A 59 TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3333) covalent geometry : angle 0.61310 / 0.28 ( 4615) hydrogen bonds : bond 0.04317 / 2.79 ( 238) hydrogen bonds : angle 3.81856 / 2.90 ( 714) *********************** 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 95 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.104 Fit side-chains REVERT: A 45 GLU cc_start: 0.8340 (tt0) cc_final: 0.8065 (tt0) REVERT: A 123 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 277 ASN cc_start: 0.8674 (m-40) cc_final: 0.8407 (m110) REVERT: A 287 TYR cc_start: 0.7874 (m-10) cc_final: 0.7544 (m-10) REVERT: A 293 ASN cc_start: 0.8366 (t0) cc_final: 0.8103 (t0) REVERT: A 294 GLU cc_start: 0.7884 (tp30) cc_final: 0.7631 (tp30) REVERT: A 306 ASN cc_start: 0.8456 (m-40) cc_final: 0.7901 (t0) REVERT: A 310 ASP cc_start: 0.9114 (t0) cc_final: 0.8795 (t0) REVERT: A 336 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7436 (mmtt) REVERT: A 346 GLN cc_start: 0.8703 (mt0) cc_final: 0.8168 (mt0) REVERT: A 412 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8788 (t) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.0380 time to fit residues: 4.4417 Evaluate side-chains 92 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 chunk 21 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.3457 r_free = 0.3457 target = 0.121715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.108166 restraints weight = 5707.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111615 restraints weight = 2372.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113869 restraints weight = 1289.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115430 restraints weight = 827.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116386 restraints weight = 581.218| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3333 Z= 0.122 Angle : 0.602 7.529 4615 Z= 0.276 Chirality : 0.036 0.143 586 Planarity : 0.004 0.043 521 Dihedral : 9.204 110.190 450 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.88 % Allowed : 29.45 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.42), residues: 394 helix: 2.69 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.81 (0.75), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.027 0.002 TYR A 366 PHE 0.008 0.001 PHE A 59 TRP 0.010 0.001 TRP A 363 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 3333) covalent geometry : angle 0.60161 / 0.28 ( 4615) hydrogen bonds : bond 0.04070 / 2.64 ( 238) hydrogen bonds : angle 3.76968 / 2.88 ( 714) *********************** 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 96 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.076 Fit side-chains REVERT: A 45 GLU cc_start: 0.8351 (tt0) cc_final: 0.8082 (tt0) REVERT: A 141 PHE cc_start: 0.8829 (t80) cc_final: 0.8172 (t80) REVERT: A 277 ASN cc_start: 0.8599 (m-40) cc_final: 0.8394 (m110) REVERT: A 287 TYR cc_start: 0.7869 (m-10) cc_final: 0.7515 (m-10) REVERT: A 293 ASN cc_start: 0.8330 (t0) cc_final: 0.7926 (t0) REVERT: A 294 GLU cc_start: 0.7832 (tp30) cc_final: 0.7487 (tp30) REVERT: A 306 ASN cc_start: 0.8442 (m-40) cc_final: 0.7900 (t0) REVERT: A 310 ASP cc_start: 0.9144 (t0) cc_final: 0.8815 (t0) REVERT: A 336 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7297 (mmtt) REVERT: A 346 GLN cc_start: 0.8697 (mt0) cc_final: 0.8215 (mt0) REVERT: A 393 LYS cc_start: 0.8484 (tppt) cc_final: 0.8118 (tppt) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.0321 time to fit residues: 3.8186 Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.123992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110320 restraints weight = 5698.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113871 restraints weight = 2390.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116073 restraints weight = 1285.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117584 restraints weight = 823.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118675 restraints weight = 586.855| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3333 Z= 0.117 Angle : 0.595 8.698 4615 Z= 0.273 Chirality : 0.035 0.146 586 Planarity : 0.004 0.043 521 Dihedral : 9.193 110.160 450 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.56 % Allowed : 30.42 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.43), residues: 394 helix: 2.71 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.81 (0.74), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.027 0.002 TYR A 366 PHE 0.006 0.001 PHE A 141 TRP 0.010 0.001 TRP A 363 HIS 0.003 0.000 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 3333) covalent geometry : angle 0.59480 / 0.27 ( 4615) hydrogen bonds : bond 0.03833 / 2.50 ( 238) hydrogen bonds : angle 3.74693 / 2.87 ( 714) *********************** 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 100 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.097 Fit side-chains REVERT: A 45 GLU cc_start: 0.8296 (tt0) cc_final: 0.8001 (tt0) REVERT: A 122 MET cc_start: 0.7840 (tmm) cc_final: 0.7623 (tmm) REVERT: A 181 SER cc_start: 0.8951 (m) cc_final: 0.8348 (p) REVERT: A 277 ASN cc_start: 0.8574 (m-40) cc_final: 0.8365 (m-40) REVERT: A 287 TYR cc_start: 0.7715 (m-10) cc_final: 0.7378 (m-10) REVERT: A 293 ASN cc_start: 0.8320 (t0) cc_final: 0.8099 (t0) REVERT: A 294 GLU cc_start: 0.7750 (tp30) cc_final: 0.7527 (tp30) REVERT: A 306 ASN cc_start: 0.8434 (m-40) cc_final: 0.7879 (t0) REVERT: A 310 ASP cc_start: 0.9128 (t0) cc_final: 0.8842 (t0) REVERT: A 313 SER cc_start: 0.9303 (OUTLIER) cc_final: 0.9014 (p) REVERT: A 336 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7227 (mmtt) REVERT: A 346 GLN cc_start: 0.8680 (mt0) cc_final: 0.8241 (mt0) REVERT: A 363 TRP cc_start: 0.7489 (m-10) cc_final: 0.7256 (m-10) REVERT: A 366 TYR cc_start: 0.8263 (m-80) cc_final: 0.7943 (m-80) outliers start: 11 outliers final: 7 residues processed: 93 average time/residue: 0.0348 time to fit residues: 4.3924 Evaluate side-chains 93 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.3473 r_free = 0.3473 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108746 restraints weight = 5742.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112260 restraints weight = 2440.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114584 restraints weight = 1344.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115847 restraints weight = 862.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117000 restraints weight = 644.460| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3333 Z= 0.134 Angle : 0.627 8.822 4615 Z= 0.290 Chirality : 0.036 0.162 586 Planarity : 0.004 0.043 521 Dihedral : 9.166 110.298 450 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.91 % Allowed : 32.04 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.43), residues: 394 helix: 2.70 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.93 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.028 0.002 TYR A 149 PHE 0.008 0.001 PHE A 125 TRP 0.010 0.001 TRP A 363 HIS 0.002 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3333) covalent geometry : angle 0.62743 / 0.29 ( 4615) hydrogen bonds : bond 0.04061 / 2.65 ( 238) hydrogen bonds : angle 3.84594 / 2.94 ( 714) *********************** 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 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.104 Fit side-chains REVERT: A 45 GLU cc_start: 0.8326 (tt0) cc_final: 0.8060 (tt0) REVERT: A 277 ASN cc_start: 0.8585 (m-40) cc_final: 0.8299 (m-40) REVERT: A 287 TYR cc_start: 0.7894 (m-10) cc_final: 0.7558 (m-10) REVERT: A 293 ASN cc_start: 0.8277 (t0) cc_final: 0.8027 (t0) REVERT: A 294 GLU cc_start: 0.7794 (tp30) cc_final: 0.7530 (tp30) REVERT: A 306 ASN cc_start: 0.8465 (m-40) cc_final: 0.7912 (t0) REVERT: A 310 ASP cc_start: 0.9158 (t0) cc_final: 0.8817 (t0) REVERT: A 366 TYR cc_start: 0.8311 (m-80) cc_final: 0.7966 (m-80) outliers start: 9 outliers final: 8 residues processed: 85 average time/residue: 0.0355 time to fit residues: 4.1321 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 ASN ** 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 = 0.3466 r_free = 0.3466 target = 0.122619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108901 restraints weight = 5706.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112365 restraints weight = 2423.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114552 restraints weight = 1329.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116115 restraints weight = 864.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117145 restraints weight = 612.780| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 3333 Z= 0.150 Angle : 0.613 6.936 4615 Z= 0.293 Chirality : 0.036 0.166 586 Planarity : 0.004 0.043 521 Dihedral : 9.183 110.347 450 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.91 % Allowed : 31.07 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.42), residues: 394 helix: 2.63 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.88 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 133 TYR 0.032 0.002 TYR A 149 PHE 0.013 0.001 PHE A 141 TRP 0.012 0.001 TRP A 363 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 3333) covalent geometry : angle 0.61338 / 0.29 ( 4615) hydrogen bonds : bond 0.04174 / 2.73 ( 238) hydrogen bonds : angle 3.86724 / 2.94 ( 714) ********************** 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 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.105 Fit side-chains REVERT: A 45 GLU cc_start: 0.8320 (tt0) cc_final: 0.8043 (tt0) REVERT: A 141 PHE cc_start: 0.8793 (t80) cc_final: 0.8072 (t80) REVERT: A 287 TYR cc_start: 0.7855 (m-10) cc_final: 0.7490 (m-10) REVERT: A 293 ASN cc_start: 0.8294 (t0) cc_final: 0.8038 (t0) REVERT: A 294 GLU cc_start: 0.7797 (tp30) cc_final: 0.7526 (tp30) REVERT: A 306 ASN cc_start: 0.8477 (m-40) cc_final: 0.7932 (t0) REVERT: A 310 ASP cc_start: 0.9140 (t0) cc_final: 0.8792 (t0) REVERT: A 346 GLN cc_start: 0.8744 (mt0) cc_final: 0.8304 (mt0) REVERT: A 363 TRP cc_start: 0.7521 (m-10) cc_final: 0.7313 (m-10) REVERT: A 366 TYR cc_start: 0.8329 (m-80) cc_final: 0.8052 (m-80) REVERT: A 393 LYS cc_start: 0.8614 (tppt) cc_final: 0.8367 (ttpt) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.0331 time to fit residues: 3.9842 Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.110001 restraints weight = 5742.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113560 restraints weight = 2417.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115762 restraints weight = 1301.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117317 restraints weight = 839.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118316 restraints weight = 594.646| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3333 Z= 0.120 Angle : 0.588 6.987 4615 Z= 0.276 Chirality : 0.036 0.152 586 Planarity : 0.004 0.043 521 Dihedral : 9.162 110.426 450 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.59 % Allowed : 31.07 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.42), residues: 394 helix: 2.73 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.85 (0.71), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 133 TYR 0.027 0.002 TYR A 366 PHE 0.016 0.001 PHE A 141 TRP 0.013 0.001 TRP A 270 HIS 0.002 0.000 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 3333) covalent geometry : angle 0.58786 / 0.28 ( 4615) hydrogen bonds : bond 0.03885 / 2.56 ( 238) hydrogen bonds : angle 3.76970 / 2.85 ( 714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 641.42 seconds wall clock time: 11 minutes 42.28 seconds (702.28 seconds total)