Starting phenix.real_space_refine on Fri Jul 25 23:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et6_28586/07_2025/8et6_28586_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et6_28586/07_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_28586/07_2025/8et6_28586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et6_28586/07_2025/8et6_28586.map" model { file = "/net/cci-nas-00/data/ceres_data/8et6_28586/07_2025/8et6_28586_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et6_28586/07_2025/8et6_28586_trim.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} 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: 4.16, per 1000 atoms: 0.51 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: 2.20 Conformation dependent library (CDL) restraints added in 698.7 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 76.7% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 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: 2.51 Time building geometry restraints manager: 2.58 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: 0.330 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: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.420 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 428 PHE 0.012 0.001 PHE A 22 TYR 0.028 0.001 TYR A 72 ARG 0.002 0.000 ARG A 462 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 2.92674 ( 3) link_BETA1-4 : bond 0.01775 ( 1) link_BETA1-4 : angle 7.25605 ( 3) hydrogen bonds : bond 0.16975 ( 256) hydrogen bonds : angle 5.57291 ( 753) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.97280 ( 6) covalent geometry : bond 0.00289 ( 4193) covalent geometry : angle 0.53060 ( 5724) *********************** 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 : 0.626 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: 0.6419 (tmt170) REVERT: A 488 MET cc_start: 0.7311 (mmm) cc_final: 0.7058 (mmm) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3821 time to fit residues: 59.9123 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 : 0.963 ------------------------------------------------------------------------------- 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 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.197898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.158620 restraints weight = 13080.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165443 restraints weight = 5978.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.169914 restraints weight = 3701.596| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4198 Z= 0.159 Angle : 0.589 7.098 5736 Z= 0.308 Chirality : 0.036 0.162 674 Planarity : 0.005 0.041 707 Dihedral : 6.253 50.734 614 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.65 % Allowed : 16.04 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.37), residues: 530 helix: 1.30 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.74 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.003 0.001 HIS A 304 PHE 0.014 0.002 PHE A 22 TYR 0.010 0.001 TYR A 240 ARG 0.004 0.001 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 1) link_NAG-ASN : angle 3.24047 ( 3) link_BETA1-4 : bond 0.01782 ( 1) link_BETA1-4 : angle 4.21258 ( 3) hydrogen bonds : bond 0.05439 ( 256) hydrogen bonds : angle 4.54166 ( 753) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.36589 ( 6) covalent geometry : bond 0.00346 ( 4193) covalent geometry : angle 0.57632 ( 5724) *********************** 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 99 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.661 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: 0.8437 (mttt) cc_final: 0.7837 (mptt) REVERT: A 27 LEU cc_start: 0.8552 (tt) cc_final: 0.8234 (tp) REVERT: A 399 ARG cc_start: 0.7233 (mmm-85) cc_final: 0.6597 (tmt170) REVERT: A 482 PHE cc_start: 0.7950 (m-10) cc_final: 0.7739 (m-10) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2921 time to fit residues: 35.4974 Evaluate side-chains 95 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4159 r_free = 0.4159 target = 0.195475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156366 restraints weight = 13486.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163255 restraints weight = 6066.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.167425 restraints weight = 3710.437| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4198 Z= 0.145 Angle : 0.543 6.488 5736 Z= 0.285 Chirality : 0.035 0.135 674 Planarity : 0.005 0.039 707 Dihedral : 5.512 47.778 614 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.37), residues: 530 helix: 1.51 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.75 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 354 HIS 0.002 0.001 HIS A 304 PHE 0.014 0.001 PHE A 22 TYR 0.010 0.001 TYR A 240 ARG 0.003 0.000 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 1) link_NAG-ASN : angle 1.76266 ( 3) link_BETA1-4 : bond 0.00950 ( 1) link_BETA1-4 : angle 2.76854 ( 3) hydrogen bonds : bond 0.05101 ( 256) hydrogen bonds : angle 4.35737 ( 753) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.31287 ( 6) covalent geometry : bond 0.00318 ( 4193) covalent geometry : angle 0.53836 ( 5724) *********************** 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 : 0.575 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 19 LYS cc_start: 0.8427 (mttt) cc_final: 0.7782 (mptt) REVERT: A 27 LEU cc_start: 0.8575 (tt) cc_final: 0.8262 (tp) REVERT: A 73 THR cc_start: 0.7604 (p) cc_final: 0.7373 (p) REVERT: A 171 ASP cc_start: 0.7433 (m-30) cc_final: 0.7219 (t0) REVERT: A 399 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.6610 (tmt170) REVERT: A 482 PHE cc_start: 0.7908 (m-10) cc_final: 0.7701 (m-10) REVERT: A 488 MET cc_start: 0.6859 (mmm) cc_final: 0.6640 (mmm) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.2782 time to fit residues: 33.5785 Evaluate side-chains 93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.0040 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.189654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.149101 restraints weight = 13387.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155880 restraints weight = 6240.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160227 restraints weight = 3892.635| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4198 Z= 0.129 Angle : 0.512 6.463 5736 Z= 0.269 Chirality : 0.034 0.132 674 Planarity : 0.005 0.037 707 Dihedral : 5.200 44.708 614 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.37), residues: 530 helix: 1.62 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.67 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 354 HIS 0.002 0.000 HIS A 304 PHE 0.013 0.001 PHE A 22 TYR 0.013 0.001 TYR A 240 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00869 ( 1) link_NAG-ASN : angle 1.29546 ( 3) link_BETA1-4 : bond 0.00940 ( 1) link_BETA1-4 : angle 2.61095 ( 3) hydrogen bonds : bond 0.04714 ( 256) hydrogen bonds : angle 4.22525 ( 753) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.29390 ( 6) covalent geometry : bond 0.00284 ( 4193) covalent geometry : angle 0.50855 ( 5724) *********************** 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 95 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.555 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 19 LYS cc_start: 0.8423 (mttt) cc_final: 0.7914 (mtmm) REVERT: A 27 LEU cc_start: 0.8442 (tt) cc_final: 0.8202 (tp) REVERT: A 73 THR cc_start: 0.7683 (p) cc_final: 0.7464 (p) REVERT: A 488 MET cc_start: 0.6775 (mmm) cc_final: 0.6545 (mmm) outliers start: 11 outliers final: 11 residues processed: 90 average time/residue: 0.3225 time to fit residues: 38.0189 Evaluate side-chains 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 281 CYS 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 36 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.188846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.149187 restraints weight = 13391.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155526 restraints weight = 6302.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159484 restraints weight = 4009.220| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3559 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= 0.152 Angle : 0.518 5.386 5736 Z= 0.276 Chirality : 0.035 0.127 674 Planarity : 0.004 0.037 707 Dihedral : 4.984 43.533 614 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.07 % Allowed : 16.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.37), residues: 530 helix: 1.61 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.67 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 217 HIS 0.002 0.001 HIS A 304 PHE 0.014 0.001 PHE A 22 TYR 0.012 0.001 TYR A 240 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 1) link_NAG-ASN : angle 1.12453 ( 3) link_BETA1-4 : bond 0.00653 ( 1) link_BETA1-4 : angle 2.31108 ( 3) hydrogen bonds : bond 0.04779 ( 256) hydrogen bonds : angle 4.24703 ( 753) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.32304 ( 6) covalent geometry : bond 0.00343 ( 4193) covalent geometry : angle 0.51552 ( 5724) *********************** 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 91 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.650 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 19 LYS cc_start: 0.8345 (mttt) cc_final: 0.7767 (mtmm) REVERT: A 27 LEU cc_start: 0.8118 (tt) cc_final: 0.7901 (tp) REVERT: A 488 MET cc_start: 0.6645 (mmm) cc_final: 0.6400 (mmm) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.2786 time to fit residues: 32.0814 Evaluate side-chains 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 171 ASP 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 48 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.179216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136595 restraints weight = 13711.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.142686 restraints weight = 6735.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146559 restraints weight = 4405.253| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3710 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= 0.120 Angle : 0.499 5.869 5736 Z= 0.261 Chirality : 0.034 0.127 674 Planarity : 0.004 0.037 707 Dihedral : 4.698 42.364 614 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.30 % Allowed : 17.45 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.37), residues: 530 helix: 1.71 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.69 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 125 HIS 0.002 0.000 HIS A 304 PHE 0.013 0.001 PHE A 22 TYR 0.014 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 1) link_NAG-ASN : angle 1.02662 ( 3) link_BETA1-4 : bond 0.00760 ( 1) link_BETA1-4 : angle 2.01110 ( 3) hydrogen bonds : bond 0.04452 ( 256) hydrogen bonds : angle 4.08138 ( 753) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.25022 ( 6) covalent geometry : bond 0.00263 ( 4193) covalent geometry : angle 0.49706 ( 5724) *********************** 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 98 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.572 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: A 19 LYS cc_start: 0.8510 (mttt) cc_final: 0.7978 (mtmm) REVERT: A 27 LEU cc_start: 0.8347 (tt) cc_final: 0.8097 (tp) REVERT: A 488 MET cc_start: 0.6731 (mmm) cc_final: 0.6500 (mmm) outliers start: 14 outliers final: 14 residues processed: 91 average time/residue: 0.2619 time to fit residues: 32.6147 Evaluate side-chains 93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 171 ASP Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 227 PHE 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 417 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.188717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.148142 restraints weight = 13474.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154517 restraints weight = 6298.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158591 restraints weight = 3988.028| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3857 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= 0.127 Angle : 0.505 6.175 5736 Z= 0.265 Chirality : 0.034 0.125 674 Planarity : 0.004 0.037 707 Dihedral : 4.613 41.476 614 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 19.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.37), residues: 530 helix: 1.76 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.70 (0.47), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.002 0.001 HIS A 428 PHE 0.013 0.001 PHE A 22 TYR 0.020 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 1) link_NAG-ASN : angle 1.20900 ( 3) link_BETA1-4 : bond 0.00728 ( 1) link_BETA1-4 : angle 1.83561 ( 3) hydrogen bonds : bond 0.04413 ( 256) hydrogen bonds : angle 4.08359 ( 753) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.25852 ( 6) covalent geometry : bond 0.00279 ( 4193) covalent geometry : angle 0.50268 ( 5724) *********************** 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 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8374 (mttt) cc_final: 0.7838 (mtmm) REVERT: A 27 LEU cc_start: 0.8225 (tt) cc_final: 0.7997 (tp) REVERT: A 488 MET cc_start: 0.6711 (mmm) cc_final: 0.6476 (mmm) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.3081 time to fit residues: 34.6009 Evaluate side-chains 89 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 171 ASP 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 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 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.190582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151770 restraints weight = 13515.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158076 restraints weight = 6257.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.162003 restraints weight = 3934.317| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3995 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= 0.123 Angle : 0.503 5.749 5736 Z= 0.264 Chirality : 0.034 0.125 674 Planarity : 0.004 0.037 707 Dihedral : 4.432 40.344 614 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.83 % Allowed : 18.40 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.37), residues: 530 helix: 1.79 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.70 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 125 HIS 0.002 0.001 HIS A 304 PHE 0.012 0.001 PHE A 22 TYR 0.015 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 1) link_NAG-ASN : angle 1.23886 ( 3) link_BETA1-4 : bond 0.00713 ( 1) link_BETA1-4 : angle 1.74221 ( 3) hydrogen bonds : bond 0.04326 ( 256) hydrogen bonds : angle 4.02572 ( 753) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.24175 ( 6) covalent geometry : bond 0.00272 ( 4193) covalent geometry : angle 0.50060 ( 5724) *********************** 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 93 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.630 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 19 LYS cc_start: 0.8406 (mttt) cc_final: 0.7905 (mtmm) REVERT: A 27 LEU cc_start: 0.8285 (tt) cc_final: 0.8052 (tp) REVERT: A 488 MET cc_start: 0.6699 (mmm) cc_final: 0.6454 (mmm) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.2637 time to fit residues: 31.1110 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 171 ASP 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 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 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.0670 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.194294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153532 restraints weight = 13699.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160381 restraints weight = 6177.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164679 restraints weight = 3842.027| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4198 Z= 0.110 Angle : 0.494 6.147 5736 Z= 0.257 Chirality : 0.033 0.128 674 Planarity : 0.004 0.036 707 Dihedral : 4.235 38.912 614 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.12 % Allowed : 19.10 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.38), residues: 530 helix: 1.87 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.66 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 125 HIS 0.001 0.000 HIS A 367 PHE 0.012 0.001 PHE A 22 TYR 0.018 0.001 TYR A 240 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 1) link_NAG-ASN : angle 1.24467 ( 3) link_BETA1-4 : bond 0.00661 ( 1) link_BETA1-4 : angle 1.55654 ( 3) hydrogen bonds : bond 0.04113 ( 256) hydrogen bonds : angle 3.92797 ( 753) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.21441 ( 6) covalent geometry : bond 0.00241 ( 4193) covalent geometry : angle 0.49250 ( 5724) *********************** 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 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.662 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: 0.8208 (tt) cc_final: 0.7977 (tp) REVERT: A 360 LEU cc_start: 0.8219 (tp) cc_final: 0.7932 (mt) REVERT: A 488 MET cc_start: 0.6697 (mmm) cc_final: 0.6455 (mmm) outliers start: 9 outliers final: 9 residues processed: 83 average time/residue: 0.2658 time to fit residues: 29.4262 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 171 ASP Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 337 LEU 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 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5648 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.193871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.153490 restraints weight = 13527.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.160279 restraints weight = 6092.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.164517 restraints weight = 3783.973| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4198 Z= 0.111 Angle : 0.495 6.687 5736 Z= 0.257 Chirality : 0.033 0.125 674 Planarity : 0.004 0.036 707 Dihedral : 4.127 37.629 614 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.36 % Allowed : 19.34 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.38), residues: 530 helix: 1.90 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.64 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 125 HIS 0.001 0.000 HIS A 304 PHE 0.012 0.001 PHE A 22 TYR 0.015 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 1) link_NAG-ASN : angle 1.32283 ( 3) link_BETA1-4 : bond 0.00629 ( 1) link_BETA1-4 : angle 1.46105 ( 3) hydrogen bonds : bond 0.04055 ( 256) hydrogen bonds : angle 3.90197 ( 753) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.23822 ( 6) covalent geometry : bond 0.00246 ( 4193) covalent geometry : angle 0.49314 ( 5724) ********************** 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 88 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.585 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: A 19 LYS cc_start: 0.8429 (mttt) cc_final: 0.7863 (mtmm) REVERT: A 27 LEU cc_start: 0.8204 (tt) cc_final: 0.7976 (tp) outliers start: 10 outliers final: 10 residues processed: 84 average time/residue: 0.2529 time to fit residues: 28.2941 Evaluate side-chains 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 171 ASP 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 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 50 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 346 HIS ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.190865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150915 restraints weight = 13572.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157372 restraints weight = 6362.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161562 restraints weight = 4029.727| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4198 Z= 0.130 Angle : 0.511 7.071 5736 Z= 0.268 Chirality : 0.034 0.126 674 Planarity : 0.004 0.035 707 Dihedral : 4.134 36.773 614 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 18.87 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.38), residues: 530 helix: 1.85 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -1.66 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 429 HIS 0.001 0.001 HIS A 367 PHE 0.013 0.001 PHE A 22 TYR 0.015 0.001 TYR A 240 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00455 ( 1) link_NAG-ASN : angle 1.43283 ( 3) link_BETA1-4 : bond 0.00561 ( 1) link_BETA1-4 : angle 1.37332 ( 3) hydrogen bonds : bond 0.04220 ( 256) hydrogen bonds : angle 3.97664 ( 753) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.24425 ( 6) covalent geometry : bond 0.00293 ( 4193) covalent geometry : angle 0.50921 ( 5724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.67 seconds wall clock time: 61 minutes 21.50 seconds (3681.50 seconds total)