Starting phenix.real_space_refine on Fri Aug 22 21:49:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586.map" model { file = "/net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et6_28586/08_2025/8et6_28586_trim.cif" } resolution = 3.57 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= 0.003 sd= 0.061 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 2681 2.51 5 N 669 2.21 5 O 706 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8092 Number of models: 1 Model: "" Number of chains: 2 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 Time building chain proxies: 1.82, per 1000 atoms: 0.22 Number of scatterers: 8092 At special positions: 0 Unit cell: (113.4, 56.16, 70.2, 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 706 8.00 N 669 7.00 C 2681 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=2.03 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: 0.67 Conformation dependent library (CDL) restraints added in 230.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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 76.7% 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 11 Processing helix chain 'A' and resid 15 through 30 Processing helix chain 'A' and resid 31 through 38 removed outlier: 4.556A pdb=" N ILE A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 4.173A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.609A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.769A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 4.364A 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: 4.268A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.692A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.856A pdb=" N MET A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.556A pdb=" N VAL A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 276 removed outlier: 3.900A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.813A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' 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: 3.556A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.946A 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 386 through 401 removed outlier: 3.507A pdb=" N ALA A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.778A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 457 removed outlier: 4.251A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 491 removed outlier: 4.037A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.575A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.987A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.703A 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 50 256 hydrogen bonds defined for protein. 753 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: 1.69 Time building geometry restraints manager: 0.90 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: 11 1.23 - 1.42: 1754 1.42 - 1.62: 2394 1.62 - 1.81: 43 Bond restraints: 8200 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.378 0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " ideal model delta sigma weight residual 1.532 1.505 0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C ILE A 461 " pdb=" O ILE A 461 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.19e-02 7.06e+03 1.24e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 1.03e+00 ... (remaining 8195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 13820 1.11 - 2.22: 915 2.22 - 3.33: 43 3.33 - 4.44: 14 4.44 - 5.55: 7 Bond angle restraints: 14799 Sorted by residual: angle pdb=" CA TYR A 72 " pdb=" CB TYR A 72 " pdb=" CG TYR A 72 " ideal model delta sigma weight residual 113.90 119.45 -5.55 1.80e+00 3.09e-01 9.50e+00 angle pdb=" N VAL A 282 " pdb=" CA VAL A 282 " pdb=" C VAL A 282 " ideal model delta sigma weight residual 107.76 110.31 -2.55 1.01e+00 9.80e-01 6.39e+00 angle pdb=" C VAL A 40 " pdb=" N PHE A 41 " pdb=" CA PHE A 41 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.75e+00 angle pdb=" CB ASP A 378 " pdb=" CG ASP A 378 " pdb=" OD2 ASP A 378 " ideal model delta sigma weight residual 118.40 122.96 -4.56 2.30e+00 1.89e-01 3.92e+00 angle pdb=" OD1 ASP A 378 " pdb=" CG ASP A 378 " pdb=" OD2 ASP A 378 " ideal model delta sigma weight residual 122.90 118.54 4.36 2.40e+00 1.74e-01 3.29e+00 ... (remaining 14794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3598 17.14 - 34.28: 209 34.28 - 51.42: 80 51.42 - 68.55: 47 68.55 - 85.69: 1 Dihedral angle restraints: 3935 sinusoidal: 2079 harmonic: 1856 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 62.81 30.19 1 1.00e+01 1.00e-02 1.30e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -115.86 29.86 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CG LYS A 214 " pdb=" CD LYS A 214 " pdb=" CE LYS A 214 " pdb=" NZ LYS A 214 " ideal model delta sinusoidal sigma weight residual 180.00 124.89 55.11 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 3932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 646 0.080 - 0.161: 27 0.161 - 0.241: 0 0.241 - 0.321: 0 0.321 - 0.402: 1 Chirality restraints: 674 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 71 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA TYR A 72 " pdb=" N TYR A 72 " pdb=" C TYR A 72 " pdb=" CB TYR A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-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 2.40 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 671 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 72 " -0.021 2.00e-02 2.50e+03 1.01e-02 3.06e+00 pdb=" CG TYR A 72 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 72 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 72 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 72 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 72 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 72 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 72 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 72 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR A 72 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 72 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 74 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 75 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 312 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 313 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.021 5.00e-02 4.00e+02 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 511 2.21 - 2.81: 16588 2.81 - 3.41: 21649 3.41 - 4.00: 26619 4.00 - 4.60: 41595 Nonbonded interactions: 106962 Sorted by model distance: nonbonded pdb=" O CYS A 26 " pdb=" HG SER A 29 " model vdw 1.615 2.450 nonbonded pdb=" O ASP A 144 " pdb=" H LYS A 147 " model vdw 1.743 2.450 nonbonded pdb=" OD1 ASP A 198 " pdb=" H TYR A 199 " model vdw 1.747 2.450 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.764 2.450 nonbonded pdb=" O GLY A 507 " pdb=" HG1 THR A 510 " model vdw 1.770 2.450 ... (remaining 106957 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 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: 0.700 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: 0.060 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.340 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 : 0.003 0.028 4198 Z= 0.141 Angle : 0.560 12.522 5736 Z= 0.291 Chirality : 0.038 0.402 674 Planarity : 0.004 0.040 707 Dihedral : 11.902 85.694 1474 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.47 % Allowed : 8.02 % Favored : 91.51 % 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 aren not related in a simple way. whole: 0.54 (0.36), residues: 530 helix: 1.15 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 462 TYR 0.028 0.001 TYR A 72 PHE 0.012 0.001 PHE A 22 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4193) covalent geometry : angle 0.53060 ( 5724) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.97280 ( 6) hydrogen bonds : bond 0.16975 ( 256) hydrogen bonds : angle 5.57291 ( 753) link_BETA1-4 : bond 0.01775 ( 1) link_BETA1-4 : angle 7.25605 ( 3) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 2.92674 ( 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 126 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.204 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 ARG cc_start: 0.6817 (mmm-85) cc_final: 0.6422 (tmt170) REVERT: A 488 MET cc_start: 0.7311 (mmm) cc_final: 0.7056 (mmm) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.1740 time to fit residues: 26.9497 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 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 = 0.4124 r_free = 0.4124 target = 0.192211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153018 restraints weight = 13321.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159667 restraints weight = 6212.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164005 restraints weight = 3886.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166258 restraints weight = 2890.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.168221 restraints weight = 2437.134| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4198 Z= 0.158 Angle : 0.592 7.272 5736 Z= 0.308 Chirality : 0.036 0.162 674 Planarity : 0.005 0.047 707 Dihedral : 6.485 53.002 614 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.65 % Allowed : 16.75 % Favored : 81.60 % 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 aren not related in a simple way. whole: 0.63 (0.37), residues: 530 helix: 1.31 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.010 0.001 TYR A 72 PHE 0.014 0.002 PHE A 22 TRP 0.004 0.001 TRP A 125 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4193) covalent geometry : angle 0.57987 ( 5724) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.39247 ( 6) hydrogen bonds : bond 0.05560 ( 256) hydrogen bonds : angle 4.60179 ( 753) link_BETA1-4 : bond 0.01366 ( 1) link_BETA1-4 : angle 4.30556 ( 3) link_NAG-ASN : bond 0.00328 ( 1) link_NAG-ASN : angle 2.98687 ( 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 101 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.202 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8431 (mttt) cc_final: 0.7939 (mtmm) REVERT: A 27 LEU cc_start: 0.8353 (tt) cc_final: 0.8143 (tp) REVERT: A 399 ARG cc_start: 0.7202 (mmm-85) cc_final: 0.6546 (tmt170) REVERT: A 482 PHE cc_start: 0.8001 (m-10) cc_final: 0.7786 (m-10) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.1404 time to fit residues: 17.7664 Evaluate side-chains 96 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 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 = 0.4158 r_free = 0.4158 target = 0.193794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156200 restraints weight = 13172.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.162584 restraints weight = 6089.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166699 restraints weight = 3792.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169125 restraints weight = 2821.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170877 restraints weight = 2346.255| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4198 Z= 0.142 Angle : 0.552 7.041 5736 Z= 0.288 Chirality : 0.035 0.141 674 Planarity : 0.005 0.041 707 Dihedral : 5.621 49.161 614 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.59 % Allowed : 17.22 % Favored : 80.19 % 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 aren not related in a simple way. whole: 0.77 (0.37), residues: 530 helix: 1.47 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.77 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 175 TYR 0.010 0.001 TYR A 240 PHE 0.014 0.001 PHE A 22 TRP 0.004 0.001 TRP A 354 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4193) covalent geometry : angle 0.54443 ( 5724) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.31548 ( 6) hydrogen bonds : bond 0.05104 ( 256) hydrogen bonds : angle 4.38106 ( 753) link_BETA1-4 : bond 0.00877 ( 1) link_BETA1-4 : angle 3.55815 ( 3) link_NAG-ASN : bond 0.00442 ( 1) link_NAG-ASN : angle 1.78041 ( 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 98 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.193 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: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8596 (tt) cc_final: 0.8317 (tp) REVERT: A 398 ASP cc_start: 0.7315 (m-30) cc_final: 0.7088 (m-30) REVERT: A 399 ARG cc_start: 0.7286 (mmm-85) cc_final: 0.6668 (tmt170) REVERT: A 482 PHE cc_start: 0.7945 (m-10) cc_final: 0.7727 (m-10) REVERT: A 488 MET cc_start: 0.6886 (mmm) cc_final: 0.6674 (mmm) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1427 time to fit residues: 16.9537 Evaluate side-chains 96 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150120 restraints weight = 13637.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.156631 restraints weight = 6171.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160786 restraints weight = 3808.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163226 restraints weight = 2832.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164907 restraints weight = 2359.319| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4198 Z= 0.211 Angle : 0.602 5.944 5736 Z= 0.328 Chirality : 0.037 0.142 674 Planarity : 0.005 0.053 707 Dihedral : 5.494 44.637 614 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.83 % Allowed : 16.75 % Favored : 80.42 % 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 aren not related in a simple way. whole: 0.56 (0.37), residues: 530 helix: 1.30 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 175 TYR 0.012 0.002 TYR A 221 PHE 0.015 0.002 PHE A 22 TRP 0.006 0.001 TRP A 217 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 4193) covalent geometry : angle 0.59669 ( 5724) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.44821 ( 6) hydrogen bonds : bond 0.05627 ( 256) hydrogen bonds : angle 4.63514 ( 753) link_BETA1-4 : bond 0.00622 ( 1) link_BETA1-4 : angle 2.70000 ( 3) link_NAG-ASN : bond 0.00729 ( 1) link_NAG-ASN : angle 2.31973 ( 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 100 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.202 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: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8434 (tt) cc_final: 0.8150 (tp) REVERT: A 73 THR cc_start: 0.7652 (p) cc_final: 0.7428 (p) REVERT: A 175 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7757 (mtt90) REVERT: A 251 LEU cc_start: 0.7322 (tt) cc_final: 0.7111 (tp) REVERT: A 482 PHE cc_start: 0.8051 (m-10) cc_final: 0.7837 (m-10) REVERT: A 488 MET cc_start: 0.7074 (mmm) cc_final: 0.6856 (mmm) outliers start: 12 outliers final: 10 residues processed: 94 average time/residue: 0.1628 time to fit residues: 19.0479 Evaluate side-chains 94 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.186254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146401 restraints weight = 13259.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152790 restraints weight = 6232.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.156874 restraints weight = 3958.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159408 restraints weight = 2984.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160821 restraints weight = 2499.217| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4198 Z= 0.134 Angle : 0.543 6.918 5736 Z= 0.285 Chirality : 0.034 0.126 674 Planarity : 0.005 0.042 707 Dihedral : 5.214 44.150 614 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.07 % Allowed : 17.92 % Favored : 79.01 % 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 aren not related in a simple way. whole: 0.76 (0.37), residues: 530 helix: 1.48 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.84 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 175 TYR 0.010 0.001 TYR A 240 PHE 0.015 0.001 PHE A 22 TRP 0.004 0.001 TRP A 354 HIS 0.002 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4193) covalent geometry : angle 0.54017 ( 5724) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.36835 ( 6) hydrogen bonds : bond 0.05015 ( 256) hydrogen bonds : angle 4.33709 ( 753) link_BETA1-4 : bond 0.00906 ( 1) link_BETA1-4 : angle 2.48832 ( 3) link_NAG-ASN : bond 0.00653 ( 1) link_NAG-ASN : angle 1.15634 ( 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 96 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.209 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: symmetry clash REVERT: A 27 LEU cc_start: 0.8136 (tt) cc_final: 0.7881 (tp) REVERT: A 488 MET cc_start: 0.6885 (mmm) cc_final: 0.6626 (mmm) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1234 time to fit residues: 14.8221 Evaluate side-chains 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.185141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145623 restraints weight = 13279.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.151956 restraints weight = 6250.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155750 restraints weight = 3964.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.158439 restraints weight = 3018.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159932 restraints weight = 2519.702| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4198 Z= 0.142 Angle : 0.533 6.311 5736 Z= 0.280 Chirality : 0.035 0.127 674 Planarity : 0.004 0.037 707 Dihedral : 4.946 43.044 614 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.83 % Allowed : 18.16 % Favored : 79.01 % 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 aren not related in a simple way. whole: 0.85 (0.37), residues: 530 helix: 1.55 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 175 TYR 0.014 0.001 TYR A 240 PHE 0.014 0.001 PHE A 22 TRP 0.005 0.001 TRP A 429 HIS 0.004 0.001 HIS A 428 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4193) covalent geometry : angle 0.53048 ( 5724) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.32644 ( 6) hydrogen bonds : bond 0.04769 ( 256) hydrogen bonds : angle 4.25413 ( 753) link_BETA1-4 : bond 0.00768 ( 1) link_BETA1-4 : angle 2.06397 ( 3) link_NAG-ASN : bond 0.00601 ( 1) link_NAG-ASN : angle 1.14460 ( 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 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.212 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: symmetry clash REVERT: A 27 LEU cc_start: 0.8032 (tt) cc_final: 0.7790 (tp) REVERT: A 488 MET cc_start: 0.6695 (mmm) cc_final: 0.6431 (mmm) outliers start: 12 outliers final: 12 residues processed: 87 average time/residue: 0.1434 time to fit residues: 16.2509 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 428 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151400 restraints weight = 13640.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158163 restraints weight = 6187.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162490 restraints weight = 3844.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164984 restraints weight = 2871.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.166663 restraints weight = 2399.283| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4198 Z= 0.119 Angle : 0.517 6.435 5736 Z= 0.267 Chirality : 0.034 0.125 674 Planarity : 0.004 0.037 707 Dihedral : 4.683 42.534 614 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.59 % Allowed : 19.34 % Favored : 78.07 % 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 aren not related in a simple way. whole: 0.95 (0.37), residues: 530 helix: 1.66 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.88 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.012 0.001 TYR A 240 PHE 0.014 0.001 PHE A 22 TRP 0.004 0.001 TRP A 125 HIS 0.001 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 4193) covalent geometry : angle 0.51499 ( 5724) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.27362 ( 6) hydrogen bonds : bond 0.04450 ( 256) hydrogen bonds : angle 4.11227 ( 753) link_BETA1-4 : bond 0.00783 ( 1) link_BETA1-4 : angle 1.93247 ( 3) link_NAG-ASN : bond 0.00651 ( 1) link_NAG-ASN : angle 1.16622 ( 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.207 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 27 LEU cc_start: 0.8240 (tt) cc_final: 0.7968 (tp) REVERT: A 488 MET cc_start: 0.6668 (mmm) cc_final: 0.6437 (mmm) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.1197 time to fit residues: 13.5182 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 412 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.172425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130555 restraints weight = 13566.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136303 restraints weight = 6785.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139988 restraints weight = 4468.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142557 restraints weight = 3466.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143597 restraints weight = 2928.151| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4198 Z= 0.179 Angle : 0.561 6.310 5736 Z= 0.299 Chirality : 0.035 0.127 674 Planarity : 0.005 0.038 707 Dihedral : 4.706 40.894 614 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.30 % Allowed : 19.10 % Favored : 77.59 % 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 aren not related in a simple way. whole: 0.77 (0.37), residues: 530 helix: 1.50 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.011 0.001 TYR A 221 PHE 0.015 0.001 PHE A 22 TRP 0.005 0.001 TRP A 217 HIS 0.003 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4193) covalent geometry : angle 0.55910 ( 5724) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.33719 ( 6) hydrogen bonds : bond 0.04956 ( 256) hydrogen bonds : angle 4.30051 ( 753) link_BETA1-4 : bond 0.00645 ( 1) link_BETA1-4 : angle 1.78128 ( 3) link_NAG-ASN : bond 0.00384 ( 1) link_NAG-ASN : angle 1.50208 ( 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 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.148 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 27 LEU cc_start: 0.8054 (tt) cc_final: 0.7852 (tp) REVERT: A 467 MET cc_start: 0.8541 (mmm) cc_final: 0.8132 (mmm) REVERT: A 488 MET cc_start: 0.6671 (mmm) cc_final: 0.6416 (mmm) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.1174 time to fit residues: 13.7301 Evaluate side-chains 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 412 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 4 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 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 = 0.3936 r_free = 0.3936 target = 0.172807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131036 restraints weight = 13510.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136792 restraints weight = 6612.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140455 restraints weight = 4317.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142842 restraints weight = 3327.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.144561 restraints weight = 2819.393| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4198 Z= 0.124 Angle : 0.523 6.527 5736 Z= 0.270 Chirality : 0.034 0.125 674 Planarity : 0.004 0.037 707 Dihedral : 4.440 39.910 614 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.83 % Allowed : 19.34 % Favored : 77.83 % 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 aren not related in a simple way. whole: 1.00 (0.37), residues: 530 helix: 1.67 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.83 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.016 0.001 TYR A 240 PHE 0.014 0.001 PHE A 22 TRP 0.004 0.001 TRP A 354 HIS 0.002 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4193) covalent geometry : angle 0.52115 ( 5724) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.24700 ( 6) hydrogen bonds : bond 0.04472 ( 256) hydrogen bonds : angle 4.09378 ( 753) link_BETA1-4 : bond 0.00774 ( 1) link_BETA1-4 : angle 1.81645 ( 3) link_NAG-ASN : bond 0.00584 ( 1) link_NAG-ASN : angle 1.29580 ( 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.326 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 27 LEU cc_start: 0.8317 (tt) cc_final: 0.8009 (tp) REVERT: A 360 LEU cc_start: 0.8227 (tp) cc_final: 0.7987 (mt) REVERT: A 467 MET cc_start: 0.8714 (mmm) cc_final: 0.8272 (mmm) REVERT: A 488 MET cc_start: 0.6729 (mmm) cc_final: 0.6494 (mmm) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.1112 time to fit residues: 12.4800 Evaluate side-chains 85 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 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 = 0.3962 r_free = 0.3962 target = 0.175544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134257 restraints weight = 13403.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140090 restraints weight = 6578.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143650 restraints weight = 4291.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.146250 restraints weight = 3318.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.147474 restraints weight = 2803.651| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4198 Z= 0.110 Angle : 0.510 6.680 5736 Z= 0.262 Chirality : 0.033 0.125 674 Planarity : 0.004 0.038 707 Dihedral : 4.253 38.594 614 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.36 % Allowed : 20.05 % Favored : 77.59 % 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 aren not related in a simple way. whole: 1.16 (0.38), residues: 530 helix: 1.81 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.81 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.015 0.001 TYR A 240 PHE 0.013 0.001 PHE A 22 TRP 0.005 0.001 TRP A 125 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4193) covalent geometry : angle 0.50841 ( 5724) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.25329 ( 6) hydrogen bonds : bond 0.04164 ( 256) hydrogen bonds : angle 3.96182 ( 753) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 1.59578 ( 3) link_NAG-ASN : bond 0.00616 ( 1) link_NAG-ASN : angle 1.35425 ( 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 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.202 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 27 LEU cc_start: 0.8249 (tt) cc_final: 0.7969 (tp) REVERT: A 360 LEU cc_start: 0.8197 (tp) cc_final: 0.7965 (mt) REVERT: A 467 MET cc_start: 0.8709 (mmm) cc_final: 0.8310 (mmm) REVERT: A 488 MET cc_start: 0.6738 (mmm) cc_final: 0.6521 (mmm) outliers start: 10 outliers final: 10 residues processed: 83 average time/residue: 0.1193 time to fit residues: 13.2782 Evaluate side-chains 83 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 412 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 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 = 0.3948 r_free = 0.3948 target = 0.174148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132307 restraints weight = 13388.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138248 restraints weight = 6420.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141751 restraints weight = 4128.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.144402 restraints weight = 3207.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145762 restraints weight = 2698.066| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4198 Z= 0.118 Angle : 0.512 6.455 5736 Z= 0.264 Chirality : 0.034 0.128 674 Planarity : 0.004 0.037 707 Dihedral : 4.155 37.030 614 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.59 % Allowed : 19.58 % Favored : 77.83 % 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 aren not related in a simple way. whole: 1.21 (0.38), residues: 530 helix: 1.84 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.78 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.013 0.001 TYR A 240 PHE 0.013 0.001 PHE A 22 TRP 0.004 0.001 TRP A 125 HIS 0.001 0.000 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4193) covalent geometry : angle 0.50994 ( 5724) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.24359 ( 6) hydrogen bonds : bond 0.04176 ( 256) hydrogen bonds : angle 3.94514 ( 753) link_BETA1-4 : bond 0.00604 ( 1) link_BETA1-4 : angle 1.44157 ( 3) link_NAG-ASN : bond 0.00534 ( 1) link_NAG-ASN : angle 1.47312 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.20 seconds wall clock time: 30 minutes 10.71 seconds (1810.71 seconds total)