Starting phenix.real_space_refine on Thu Jul 2 10:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et8_28588/07_2026/8et8_28588.map" } resolution = 3.45 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= 0.001 sd= 0.039 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 2708 2.51 5 N 671 2.21 5 O 710 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s 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: 8125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8064 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'4YH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.20 Number of scatterers: 8125 At special positions: 0 Unit cell: (113.52, 58.96, 72.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 710 8.00 N 671 7.00 C 2708 6.00 H 4007 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 71 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 264.1 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 1 sheets defined 76.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.500A pdb=" N LEU A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix removed outlier: 3.998A pdb=" N GLY A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 4.129A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.555A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 4.184A pdb=" N ALA A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 145 through 173 removed outlier: 4.393A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.629A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.595A pdb=" N MET A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.605A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.528A pdb=" N LEU A 317 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.974A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.213A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 428 through 457 removed outlier: 3.919A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 4.066A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.867A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.618A pdb=" N ILE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.753A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 258 hydrogen bonds defined for protein. 762 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: 1.76 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3998 1.03 - 1.23: 12 1.23 - 1.42: 1771 1.42 - 1.62: 2410 1.62 - 1.81: 43 Bond restraints: 8234 Sorted by residual: bond pdb=" C6 4YH A 601 " pdb=" C9 4YH A 601 " ideal model delta sigma weight residual 1.425 1.356 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C32 4YH A 601 " pdb=" O23 4YH A 601 " ideal model delta sigma weight residual 1.458 1.390 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C33 4YH A 601 " pdb=" O24 4YH A 601 " ideal model delta sigma weight residual 1.459 1.395 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C31 4YH A 601 " pdb=" O20 4YH A 601 " ideal model delta sigma weight residual 1.456 1.395 0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C1 4YH A 601 " pdb=" C15 4YH A 601 " ideal model delta sigma weight residual 1.578 1.518 0.060 2.00e-02 2.50e+03 9.03e+00 ... (remaining 8229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14687 1.70 - 3.40: 130 3.40 - 5.10: 19 5.10 - 6.80: 6 6.80 - 8.50: 3 Bond angle restraints: 14845 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 111.77 108.47 3.30 1.04e+00 9.25e-01 1.01e+01 angle pdb=" C16 4YH A 601 " pdb=" C21 4YH A 601 " pdb=" C17 4YH A 601 " ideal model delta sigma weight residual 113.30 121.80 -8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" C12 4YH A 601 " pdb=" C7 4YH A 601 " pdb=" O20 4YH A 601 " ideal model delta sigma weight residual 125.76 117.49 8.27 3.00e+00 1.11e-01 7.59e+00 angle pdb=" C10 4YH A 601 " pdb=" C7 4YH A 601 " pdb=" O20 4YH A 601 " ideal model delta sigma weight residual 114.29 121.12 -6.83 3.00e+00 1.11e-01 5.18e+00 angle pdb=" C26 4YH A 601 " pdb=" C25 4YH A 601 " pdb=" N8 4YH A 601 " ideal model delta sigma weight residual 119.79 113.41 6.38 3.00e+00 1.11e-01 4.52e+00 ... (remaining 14840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.09: 3814 31.09 - 62.19: 143 62.19 - 93.28: 10 93.28 - 124.38: 1 124.38 - 155.47: 2 Dihedral angle restraints: 3970 sinusoidal: 2114 harmonic: 1856 Sorted by residual: dihedral pdb=" C29 4YH A 601 " pdb=" C1 4YH A 601 " pdb=" C15 4YH A 601 " pdb=" C3 4YH A 601 " ideal model delta sinusoidal sigma weight residual 77.20 -78.27 155.47 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C22 4YH A 601 " pdb=" C1 4YH A 601 " pdb=" C15 4YH A 601 " pdb=" C29 4YH A 601 " ideal model delta sinusoidal sigma weight residual 36.95 -169.43 -153.62 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C22 4YH A 601 " pdb=" C25 4YH A 601 " pdb=" C26 4YH A 601 " pdb=" N8 4YH A 601 " ideal model delta sinusoidal sigma weight residual 69.89 166.96 -97.07 1 3.00e+01 1.11e-03 1.20e+01 ... (remaining 3967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 445 0.027 - 0.054: 150 0.054 - 0.081: 54 0.081 - 0.108: 23 0.108 - 0.135: 3 Chirality restraints: 675 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 7.21e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 672 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 75 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO A 271 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 4YH A 601 " -0.000 2.00e-02 2.50e+03 8.14e-03 1.49e+00 pdb=" C12 4YH A 601 " 0.008 2.00e-02 2.50e+03 pdb=" C14 4YH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C17 4YH A 601 " 0.003 2.00e-02 2.50e+03 pdb=" C18 4YH A 601 " 0.006 2.00e-02 2.50e+03 pdb=" C21 4YH A 601 " -0.015 2.00e-02 2.50e+03 pdb=" C7 4YH A 601 " 0.011 2.00e-02 2.50e+03 pdb=" O20 4YH A 601 " -0.005 2.00e-02 2.50e+03 pdb=" O24 4YH A 601 " -0.011 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 281 2.17 - 2.78: 15649 2.78 - 3.39: 22673 3.39 - 3.99: 27448 3.99 - 4.60: 43192 Nonbonded interactions: 109243 Sorted by model distance: nonbonded pdb="HH21 ARG A 233 " pdb=" OE2 GLU A 455 " model vdw 1.564 2.450 nonbonded pdb=" HE ARG A 234 " pdb=" OD2 ASP A 398 " model vdw 1.647 2.450 nonbonded pdb=" O CYS A 26 " pdb=" HG SER A 29 " model vdw 1.752 2.450 nonbonded pdb=" OG1 THR A 347 " pdb=" HH TYR A 457 " model vdw 1.761 2.450 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.798 2.450 ... (remaining 109238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.490 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.005 0.069 4232 Z= 0.224 Angle : 0.598 8.501 5782 Z= 0.291 Chirality : 0.034 0.135 675 Planarity : 0.004 0.034 709 Dihedral : 14.858 155.472 1509 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.94 % Allowed : 4.25 % Favored : 94.81 % 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: 1.27 (0.37), residues: 530 helix: 1.73 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.015 0.001 TYR A 72 PHE 0.010 0.001 PHE A 275 TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 ( 4227) covalent geometry : angle 0.59427 / 0.29 ( 5770) SS BOND : bond 0.00863 / 0.44 ( 3) SS BOND : angle 1.21455 / 0.53 ( 6) hydrogen bonds : bond 0.14568 / 9.94 ( 258) hydrogen bonds : angle 5.61878 / 4.01 ( 762) link_BETA1-4 : bond 0.00212 / 0.14 ( 1) link_BETA1-4 : angle 1.03219 / 0.72 ( 3) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 2.30181 / 2.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8385 (tp) cc_final: 0.7821 (mt) REVERT: A 242 MET cc_start: 0.6546 (ttt) cc_final: 0.6258 (mtp) REVERT: A 360 LEU cc_start: 0.8556 (tp) cc_final: 0.8086 (tp) REVERT: A 393 ILE cc_start: 0.8876 (tt) cc_final: 0.8451 (tt) REVERT: A 457 TYR cc_start: 0.8361 (m-80) cc_final: 0.8085 (m-80) outliers start: 4 outliers final: 4 residues processed: 112 average time/residue: 0.1254 time to fit residues: 18.3163 Evaluate side-chains 80 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 178 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.193246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157814 restraints weight = 13102.449| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.10 r_work: 0.3653 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4232 Z= 0.159 Angle : 0.578 6.573 5782 Z= 0.307 Chirality : 0.035 0.169 675 Planarity : 0.005 0.040 709 Dihedral : 12.592 132.862 653 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.12 % Allowed : 12.74 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.37), residues: 530 helix: 1.70 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.25 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.011 0.001 TYR A 199 PHE 0.011 0.001 PHE A 275 TRP 0.006 0.001 TRP A 217 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 4227) covalent geometry : angle 0.56825 / 0.30 ( 5770) SS BOND : bond 0.00253 / 0.14 ( 3) SS BOND : angle 2.95991 / 1.83 ( 6) hydrogen bonds : bond 0.05626 / 3.76 ( 258) hydrogen bonds : angle 4.55796 / 3.23 ( 762) link_BETA1-4 : bond 0.00839 / 0.56 ( 1) link_BETA1-4 : angle 0.62394 / 0.48 ( 3) link_NAG-ASN : bond 0.00438 / 0.29 ( 1) link_NAG-ASN : angle 1.95939 / 1.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8846 (tt) cc_final: 0.8319 (mm) REVERT: A 180 LEU cc_start: 0.8397 (tp) cc_final: 0.7833 (mt) REVERT: A 242 MET cc_start: 0.7379 (ttt) cc_final: 0.7020 (mtp) REVERT: A 360 LEU cc_start: 0.8666 (tp) cc_final: 0.8115 (tp) REVERT: A 457 TYR cc_start: 0.8545 (m-80) cc_final: 0.8341 (m-80) REVERT: A 488 MET cc_start: 0.8090 (mmm) cc_final: 0.7853 (mmt) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.0788 time to fit residues: 8.7857 Evaluate side-chains 73 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 366 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.187718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.152418 restraints weight = 13150.441| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.12 r_work: 0.3592 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4232 Z= 0.146 Angle : 0.548 5.833 5782 Z= 0.288 Chirality : 0.035 0.132 675 Planarity : 0.005 0.040 709 Dihedral : 10.251 117.274 652 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.12 % Allowed : 14.39 % Favored : 83.49 % 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: 1.12 (0.37), residues: 530 helix: 1.70 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.40 (0.48), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 49 TYR 0.009 0.001 TYR A 199 PHE 0.009 0.001 PHE A 275 TRP 0.005 0.001 TRP A 217 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4227) covalent geometry : angle 0.54187 / 0.29 ( 5770) SS BOND : bond 0.00492 / 0.32 ( 3) SS BOND : angle 2.39007 / 1.26 ( 6) hydrogen bonds : bond 0.04964 / 3.31 ( 258) hydrogen bonds : angle 4.32961 / 3.05 ( 762) link_BETA1-4 : bond 0.00456 / 0.30 ( 1) link_BETA1-4 : angle 0.67999 / 0.36 ( 3) link_NAG-ASN : bond 0.00581 / 0.39 ( 1) link_NAG-ASN : angle 1.66828 / 1.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8077 (mp0) cc_final: 0.7420 (mp0) REVERT: A 180 LEU cc_start: 0.8378 (tp) cc_final: 0.7854 (mt) REVERT: A 242 MET cc_start: 0.7365 (ttt) cc_final: 0.7020 (mtp) REVERT: A 360 LEU cc_start: 0.8665 (tp) cc_final: 0.8104 (tp) REVERT: A 457 TYR cc_start: 0.8594 (m-80) cc_final: 0.8380 (m-80) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.0783 time to fit residues: 8.7692 Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.188486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153638 restraints weight = 13280.637| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.12 r_work: 0.3584 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4232 Z= 0.136 Angle : 0.527 5.494 5782 Z= 0.277 Chirality : 0.034 0.133 675 Planarity : 0.005 0.046 709 Dihedral : 9.831 114.186 652 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.65 % Allowed : 15.33 % Favored : 83.02 % 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: 1.15 (0.37), residues: 530 helix: 1.72 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.39 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 486 TYR 0.009 0.001 TYR A 199 PHE 0.010 0.001 PHE A 275 TRP 0.004 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 4227) covalent geometry : angle 0.52345 / 0.28 ( 5770) SS BOND : bond 0.00550 / 0.34 ( 3) SS BOND : angle 1.64604 / 0.78 ( 6) hydrogen bonds : bond 0.04772 / 3.18 ( 258) hydrogen bonds : angle 4.28814 / 3.03 ( 762) link_BETA1-4 : bond 0.00412 / 0.27 ( 1) link_BETA1-4 : angle 0.65187 / 0.38 ( 3) link_NAG-ASN : bond 0.00038 / 0.03 ( 1) link_NAG-ASN : angle 1.78136 / 1.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8076 (mp0) cc_final: 0.7439 (mp0) REVERT: A 180 LEU cc_start: 0.8339 (tp) cc_final: 0.7821 (mt) REVERT: A 242 MET cc_start: 0.7415 (ttt) cc_final: 0.7065 (mtp) REVERT: A 360 LEU cc_start: 0.8660 (tp) cc_final: 0.8096 (tp) REVERT: A 457 TYR cc_start: 0.8590 (m-80) cc_final: 0.8375 (m-80) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.0860 time to fit residues: 9.2416 Evaluate side-chains 77 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.153337 restraints weight = 12922.412| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.11 r_work: 0.3538 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4232 Z= 0.131 Angle : 0.530 6.467 5782 Z= 0.277 Chirality : 0.033 0.133 675 Planarity : 0.005 0.054 709 Dihedral : 9.513 111.523 650 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.12 % Allowed : 15.09 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.37), residues: 530 helix: 1.76 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 486 TYR 0.009 0.001 TYR A 199 PHE 0.009 0.001 PHE A 275 TRP 0.004 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4227) covalent geometry : angle 0.52411 / 0.28 ( 5770) SS BOND : bond 0.01384 / 0.92 ( 3) SS BOND : angle 2.10426 / 1.27 ( 6) hydrogen bonds : bond 0.04674 / 3.11 ( 258) hydrogen bonds : angle 4.23586 / 2.99 ( 762) link_BETA1-4 : bond 0.00395 / 0.26 ( 1) link_BETA1-4 : angle 0.76570 / 0.44 ( 3) link_NAG-ASN : bond 0.00125 / 0.08 ( 1) link_NAG-ASN : angle 1.72541 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8088 (mp0) cc_final: 0.7424 (mp0) REVERT: A 180 LEU cc_start: 0.8288 (tp) cc_final: 0.7780 (mt) REVERT: A 242 MET cc_start: 0.7342 (ttt) cc_final: 0.6994 (mtp) REVERT: A 360 LEU cc_start: 0.8630 (tp) cc_final: 0.8051 (tp) REVERT: A 362 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: A 457 TYR cc_start: 0.8558 (m-80) cc_final: 0.8337 (m-80) outliers start: 9 outliers final: 8 residues processed: 78 average time/residue: 0.0917 time to fit residues: 10.1691 Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 491 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.185671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150210 restraints weight = 12979.607| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.13 r_work: 0.3537 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4232 Z= 0.138 Angle : 0.530 6.467 5782 Z= 0.278 Chirality : 0.033 0.133 675 Planarity : 0.005 0.054 709 Dihedral : 9.513 111.523 650 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.12 % Allowed : 15.09 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.37), residues: 530 helix: 1.76 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 486 TYR 0.009 0.001 TYR A 199 PHE 0.009 0.001 PHE A 275 TRP 0.004 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4227) covalent geometry : angle 0.52411 / 0.28 ( 5770) SS BOND : bond 0.03700 / 2.46 ( 3) SS BOND : angle 2.22398 / 1.17 ( 6) hydrogen bonds : bond 0.04674 / 3.11 ( 258) hydrogen bonds : angle 4.23586 / 2.99 ( 762) link_BETA1-4 : bond 0.00395 / 0.26 ( 1) link_BETA1-4 : angle 0.76570 / 0.44 ( 3) link_NAG-ASN : bond 0.00125 / 0.08 ( 1) link_NAG-ASN : angle 1.72541 / 1.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8090 (mp0) cc_final: 0.7431 (mp0) REVERT: A 180 LEU cc_start: 0.8292 (tp) cc_final: 0.7784 (mt) REVERT: A 242 MET cc_start: 0.7340 (ttt) cc_final: 0.6994 (mtp) REVERT: A 360 LEU cc_start: 0.8626 (tp) cc_final: 0.8048 (tp) REVERT: A 362 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7464 (mm-40) REVERT: A 457 TYR cc_start: 0.8555 (m-80) cc_final: 0.8335 (m-80) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.0816 time to fit residues: 8.8667 Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 491 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** 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 = 0.4006 r_free = 0.4006 target = 0.183034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147607 restraints weight = 13228.015| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.12 r_work: 0.3378 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4232 Z= 0.195 Angle : 0.583 7.294 5782 Z= 0.314 Chirality : 0.036 0.131 675 Planarity : 0.005 0.056 709 Dihedral : 9.215 94.111 650 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.36 % Allowed : 16.98 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.37), residues: 530 helix: 1.54 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 486 TYR 0.010 0.002 TYR A 240 PHE 0.011 0.001 PHE A 391 TRP 0.007 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 4227) covalent geometry : angle 0.57899 / 0.31 ( 5770) SS BOND : bond 0.01132 / 0.74 ( 3) SS BOND : angle 2.06067 / 1.07 ( 6) hydrogen bonds : bond 0.05135 / 3.41 ( 258) hydrogen bonds : angle 4.48146 / 3.17 ( 762) link_BETA1-4 : bond 0.00336 / 0.22 ( 1) link_BETA1-4 : angle 0.74136 / 0.41 ( 3) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.52818 / 1.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8361 (tp) cc_final: 0.7865 (mt) REVERT: A 242 MET cc_start: 0.7480 (ttt) cc_final: 0.7108 (mtp) REVERT: A 360 LEU cc_start: 0.8699 (tp) cc_final: 0.8354 (mt) REVERT: A 362 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7483 (mm-40) REVERT: A 457 TYR cc_start: 0.8702 (m-80) cc_final: 0.8442 (m-80) REVERT: A 504 LEU cc_start: 0.8211 (tt) cc_final: 0.7973 (tt) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0830 time to fit residues: 8.7000 Evaluate side-chains 75 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 484 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** 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 = 0.4034 r_free = 0.4034 target = 0.185544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150165 restraints weight = 13006.431| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.08 r_work: 0.3406 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4232 Z= 0.143 Angle : 0.549 7.064 5782 Z= 0.292 Chirality : 0.034 0.128 675 Planarity : 0.005 0.045 709 Dihedral : 8.886 91.406 650 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 17.69 % Favored : 79.95 % 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: 0.97 (0.37), residues: 530 helix: 1.55 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 486 TYR 0.009 0.001 TYR A 72 PHE 0.009 0.001 PHE A 275 TRP 0.006 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4227) covalent geometry : angle 0.54468 / 0.29 ( 5770) SS BOND : bond 0.00536 / 0.31 ( 3) SS BOND : angle 1.76862 / 0.82 ( 6) hydrogen bonds : bond 0.04983 / 3.31 ( 258) hydrogen bonds : angle 4.37062 / 3.10 ( 762) link_BETA1-4 : bond 0.00500 / 0.33 ( 1) link_BETA1-4 : angle 0.91581 / 0.54 ( 3) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.55620 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8333 (tp) cc_final: 0.7840 (mt) REVERT: A 242 MET cc_start: 0.7429 (ttt) cc_final: 0.7070 (mtp) REVERT: A 360 LEU cc_start: 0.8685 (tp) cc_final: 0.8342 (mt) REVERT: A 362 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7449 (mm-40) REVERT: A 457 TYR cc_start: 0.8686 (m-80) cc_final: 0.8428 (m-80) REVERT: A 504 LEU cc_start: 0.8205 (tt) cc_final: 0.7957 (tt) outliers start: 10 outliers final: 9 residues processed: 71 average time/residue: 0.0807 time to fit residues: 8.0896 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 491 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.185374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149923 restraints weight = 13054.523| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4232 Z= 0.145 Angle : 0.550 7.064 5782 Z= 0.293 Chirality : 0.034 0.128 675 Planarity : 0.005 0.045 709 Dihedral : 8.886 91.406 650 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 17.69 % Favored : 79.95 % 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: 0.97 (0.37), residues: 530 helix: 1.55 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 486 TYR 0.009 0.001 TYR A 72 PHE 0.009 0.001 PHE A 275 TRP 0.006 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4227) covalent geometry : angle 0.54468 / 0.29 ( 5770) SS BOND : bond 0.02118 / 1.40 ( 3) SS BOND : angle 2.02972 / 0.99 ( 6) hydrogen bonds : bond 0.04983 / 3.31 ( 258) hydrogen bonds : angle 4.37062 / 3.10 ( 762) link_BETA1-4 : bond 0.00500 / 0.33 ( 1) link_BETA1-4 : angle 0.91581 / 0.54 ( 3) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.55620 / 1.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8324 (tp) cc_final: 0.7830 (mt) REVERT: A 242 MET cc_start: 0.7423 (ttt) cc_final: 0.7064 (mtp) REVERT: A 360 LEU cc_start: 0.8679 (tp) cc_final: 0.8338 (mt) REVERT: A 362 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: A 457 TYR cc_start: 0.8684 (m-80) cc_final: 0.8429 (m-80) REVERT: A 504 LEU cc_start: 0.8195 (tt) cc_final: 0.7949 (tt) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.0841 time to fit residues: 8.5900 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 491 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.185376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149951 restraints weight = 13013.467| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.13 r_work: 0.3403 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4232 Z= 0.145 Angle : 0.550 7.064 5782 Z= 0.293 Chirality : 0.034 0.128 675 Planarity : 0.005 0.045 709 Dihedral : 8.886 91.406 650 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 17.69 % Favored : 79.95 % 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: 0.97 (0.37), residues: 530 helix: 1.55 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 486 TYR 0.009 0.001 TYR A 72 PHE 0.009 0.001 PHE A 275 TRP 0.006 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4227) covalent geometry : angle 0.54468 / 0.29 ( 5770) SS BOND : bond 0.02118 / 1.40 ( 3) SS BOND : angle 2.02972 / 0.99 ( 6) hydrogen bonds : bond 0.04983 / 3.31 ( 258) hydrogen bonds : angle 4.37062 / 3.10 ( 762) link_BETA1-4 : bond 0.00500 / 0.33 ( 1) link_BETA1-4 : angle 0.91581 / 0.54 ( 3) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.55620 / 1.41 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8310 (tp) cc_final: 0.7815 (mt) REVERT: A 242 MET cc_start: 0.7406 (ttt) cc_final: 0.7051 (mtp) REVERT: A 360 LEU cc_start: 0.8662 (tp) cc_final: 0.8325 (mt) REVERT: A 362 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7443 (mm-40) REVERT: A 457 TYR cc_start: 0.8682 (m-80) cc_final: 0.8427 (m-80) REVERT: A 504 LEU cc_start: 0.8175 (tt) cc_final: 0.7931 (tt) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.0691 time to fit residues: 7.0783 Evaluate side-chains 78 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 491 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 39 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 48 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.185376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149927 restraints weight = 13063.553| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.13 r_work: 0.3403 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4232 Z= 0.145 Angle : 0.550 7.064 5782 Z= 0.293 Chirality : 0.034 0.128 675 Planarity : 0.005 0.045 709 Dihedral : 8.886 91.406 650 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.36 % Allowed : 17.69 % Favored : 79.95 % 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: 0.97 (0.37), residues: 530 helix: 1.55 (0.27), residues: 361 sheet: None (None), residues: 0 loop : -1.38 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 486 TYR 0.009 0.001 TYR A 72 PHE 0.009 0.001 PHE A 275 TRP 0.006 0.001 TRP A 429 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4227) covalent geometry : angle 0.54468 / 0.29 ( 5770) SS BOND : bond 0.02118 / 1.40 ( 3) SS BOND : angle 2.02972 / 0.99 ( 6) hydrogen bonds : bond 0.04983 / 3.31 ( 258) hydrogen bonds : angle 4.37062 / 3.10 ( 762) link_BETA1-4 : bond 0.00500 / 0.33 ( 1) link_BETA1-4 : angle 0.91581 / 0.54 ( 3) link_NAG-ASN : bond 0.00067 / 0.04 ( 1) link_NAG-ASN : angle 1.55620 / 1.41 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1947.42 seconds wall clock time: 33 minutes 39.28 seconds (2019.28 seconds total)