Starting phenix.real_space_refine on Sun May 11 14:54:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et6_28586/05_2025/8et6_28586_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et6_28586/05_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_28586/05_2025/8et6_28586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et6_28586/05_2025/8et6_28586.map" model { file = "/net/cci-nas-00/data/ceres_data/8et6_28586/05_2025/8et6_28586_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et6_28586/05_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-5687/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: 4.18, per 1000 atoms: 0.52 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: 2.09 Conformation dependent library (CDL) restraints added in 695.5 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: 0.59 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: 2.71 Time building geometry restraints manager: 2.52 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: 0.540 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: 0.060 Set scattering table: 0.070 Process input model: 20.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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: 24.500 ------------------------------------------------------------------------------- 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 : 0.652 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: 0.3650 time to fit residues: 56.8234 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 : 0.640 ------------------------------------------------------------------------------- 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: 0.9980 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 = 0.158624 restraints weight = 13080.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.165445 restraints weight = 5977.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169673 restraints weight = 3701.735| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 3.24046 ( 3) link_BETA1-4 : bond 0.01783 ( 1) link_BETA1-4 : angle 4.21262 ( 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 : 0.615 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: 0.7833 (mptt) REVERT: A 27 LEU cc_start: 0.8546 (tt) cc_final: 0.8229 (tp) REVERT: A 399 ARG cc_start: 0.7240 (mmm-85) cc_final: 0.6591 (tmt170) REVERT: A 482 PHE cc_start: 0.7944 (m-10) cc_final: 0.7735 (m-10) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2935 time to fit residues: 35.6854 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 : 0.635 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.197634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158805 restraints weight = 13416.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.165739 restraints weight = 6031.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.170176 restraints weight = 3667.271| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2781 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= 0.126 Angle : 0.531 6.788 5736 Z= 0.275 Chirality : 0.034 0.133 674 Planarity : 0.005 0.040 707 Dihedral : 5.560 48.352 614 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: 0.89 (0.37), residues: 530 helix: 1.56 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.73 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 354 HIS 0.001 0.001 HIS A 304 PHE 0.013 0.001 PHE A 22 TYR 0.011 0.001 TYR A 240 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.01925 ( 1) link_NAG-ASN : angle 1.05521 ( 3) link_BETA1-4 : bond 0.01040 ( 1) link_BETA1-4 : angle 3.14411 ( 3) hydrogen bonds : bond 0.04926 ( 256) hydrogen bonds : angle 4.27745 ( 753) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.28411 ( 6) covalent geometry : bond 0.00270 ( 4193) covalent geometry : angle 0.52643 ( 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 96 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 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: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8422 (mttt) cc_final: 0.7774 (mptt) REVERT: A 27 LEU cc_start: 0.8527 (tt) cc_final: 0.8250 (tp) REVERT: A 399 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6612 (tmt170) REVERT: A 482 PHE cc_start: 0.7900 (m-10) cc_final: 0.7699 (m-10) REVERT: A 488 MET cc_start: 0.6835 (mmm) cc_final: 0.6611 (mmm) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.2816 time to fit residues: 33.5782 Evaluate side-chains 92 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 0.0070 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.198707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.158977 restraints weight = 13467.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165904 restraints weight = 6122.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170449 restraints weight = 3792.245| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4198 Z= 0.122 Angle : 0.505 6.531 5736 Z= 0.264 Chirality : 0.034 0.130 674 Planarity : 0.004 0.037 707 Dihedral : 5.142 44.684 614 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.59 % Allowed : 16.51 % Favored : 80.90 % 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: 1.69 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.64 (0.47), residues: 162 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 0.012 0.001 PHE A 22 TYR 0.010 0.001 TYR A 240 ARG 0.001 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00762 ( 1) link_NAG-ASN : angle 1.09680 ( 3) link_BETA1-4 : bond 0.00847 ( 1) link_BETA1-4 : angle 2.80262 ( 3) hydrogen bonds : bond 0.04538 ( 256) hydrogen bonds : angle 4.14371 ( 753) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.27084 ( 6) covalent geometry : bond 0.00266 ( 4193) covalent geometry : angle 0.50065 ( 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 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.556 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: 0.8426 (mttt) cc_final: 0.7900 (mtmm) REVERT: A 27 LEU cc_start: 0.8477 (tt) cc_final: 0.8170 (tp) REVERT: A 488 MET cc_start: 0.6739 (mmm) cc_final: 0.6502 (mmm) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.2983 time to fit residues: 32.7073 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 : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.178478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136463 restraints weight = 13632.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142538 restraints weight = 6678.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146451 restraints weight = 4357.372| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3400 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= 0.144 Angle : 0.515 5.446 5736 Z= 0.274 Chirality : 0.035 0.125 674 Planarity : 0.005 0.038 707 Dihedral : 4.918 43.381 614 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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 (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: 1.04 (0.37), residues: 530 helix: 1.66 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.65 (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 0.013 0.001 PHE A 22 TYR 0.014 0.001 TYR A 240 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 1) link_NAG-ASN : angle 1.10929 ( 3) link_BETA1-4 : bond 0.00814 ( 1) link_BETA1-4 : angle 2.09288 ( 3) hydrogen bonds : bond 0.04712 ( 256) hydrogen bonds : angle 4.19085 ( 753) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.31818 ( 6) covalent geometry : bond 0.00324 ( 4193) covalent geometry : angle 0.51275 ( 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 92 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.591 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: 0.8334 (mttt) cc_final: 0.7750 (mtmm) REVERT: A 27 LEU cc_start: 0.8115 (tt) cc_final: 0.7893 (tp) REVERT: A 488 MET cc_start: 0.6615 (mmm) cc_final: 0.6363 (mmm) outliers start: 12 outliers final: 12 residues processed: 86 average time/residue: 0.2690 time to fit residues: 30.7876 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 : 0.610 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.185625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146057 restraints weight = 13470.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.152248 restraints weight = 6382.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156256 restraints weight = 4086.054| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3630 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= 0.118 Angle : 0.498 5.784 5736 Z= 0.261 Chirality : 0.034 0.136 674 Planarity : 0.004 0.037 707 Dihedral : 4.727 42.694 614 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.83 % Allowed : 17.69 % Favored : 79.48 % 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: 1.15 (0.37), residues: 530 helix: 1.75 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.60 (0.48), residues: 162 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 0.013 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 0.00546 ( 1) link_NAG-ASN : angle 0.93371 ( 3) link_BETA1-4 : bond 0.00643 ( 1) link_BETA1-4 : angle 1.91766 ( 3) hydrogen bonds : bond 0.04463 ( 256) hydrogen bonds : angle 4.06091 ( 753) SS BOND : bond 0.00139 ( 3) SS BOND : angle 0.25696 ( 6) covalent geometry : bond 0.00258 ( 4193) covalent geometry : angle 0.49615 ( 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 92 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.591 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: 0.8448 (mttt) cc_final: 0.7850 (mtmm) REVERT: A 27 LEU cc_start: 0.8064 (tt) cc_final: 0.7854 (tp) REVERT: A 488 MET cc_start: 0.6608 (mmm) cc_final: 0.6371 (mmm) outliers start: 12 outliers final: 12 residues processed: 85 average time/residue: 0.2733 time to fit residues: 31.2443 Evaluate side-chains 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 228 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.178079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135903 restraints weight = 13714.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.141965 restraints weight = 6732.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.145942 restraints weight = 4378.318| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3791 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= 0.131 Angle : 0.504 5.672 5736 Z= 0.266 Chirality : 0.034 0.128 674 Planarity : 0.004 0.037 707 Dihedral : 4.532 41.247 614 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 17.69 % Favored : 79.48 % 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: 1.21 (0.38), residues: 530 helix: 1.78 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.56 (0.48), residues: 162 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 0.020 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 1) link_NAG-ASN : angle 1.08331 ( 3) link_BETA1-4 : bond 0.00680 ( 1) link_BETA1-4 : angle 1.78073 ( 3) hydrogen bonds : bond 0.04448 ( 256) hydrogen bonds : angle 4.06140 ( 753) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.26515 ( 6) covalent geometry : bond 0.00294 ( 4193) covalent geometry : angle 0.50255 ( 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 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.574 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: 0.8425 (mttt) cc_final: 0.7928 (mtmm) REVERT: A 27 LEU cc_start: 0.8294 (tt) cc_final: 0.8066 (tp) REVERT: A 488 MET cc_start: 0.6763 (mmm) cc_final: 0.6527 (mmm) outliers start: 12 outliers final: 12 residues processed: 83 average time/residue: 0.2730 time to fit residues: 30.5216 Evaluate side-chains 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 472 LEU 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: 0.2980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.188953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150509 restraints weight = 13518.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156708 restraints weight = 6240.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160671 restraints weight = 3938.979| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3911 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= 0.122 Angle : 0.501 5.482 5736 Z= 0.263 Chirality : 0.034 0.127 674 Planarity : 0.004 0.037 707 Dihedral : 4.362 39.519 614 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.30 % Allowed : 17.22 % Favored : 79.48 % 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: 1.82 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.55 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 125 HIS 0.002 0.001 HIS A 367 PHE 0.012 0.001 PHE A 22 TYR 0.019 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 1) link_NAG-ASN : angle 1.07252 ( 3) link_BETA1-4 : bond 0.00656 ( 1) link_BETA1-4 : angle 1.63090 ( 3) hydrogen bonds : bond 0.04335 ( 256) hydrogen bonds : angle 4.00381 ( 753) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.24417 ( 6) covalent geometry : bond 0.00270 ( 4193) covalent geometry : angle 0.49932 ( 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 95 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.588 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 13 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6343 (mm-30) REVERT: A 19 LYS cc_start: 0.8421 (mttt) cc_final: 0.7885 (mtmm) REVERT: A 27 LEU cc_start: 0.8193 (tt) cc_final: 0.7972 (tp) REVERT: A 488 MET cc_start: 0.6679 (mmm) cc_final: 0.6419 (mmm) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.2581 time to fit residues: 30.9626 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 : 0.564 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 472 LEU 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: 0.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.190034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151586 restraints weight = 13544.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157853 restraints weight = 6250.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.161859 restraints weight = 3926.886| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4054 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= 0.122 Angle : 0.504 6.837 5736 Z= 0.264 Chirality : 0.034 0.128 674 Planarity : 0.004 0.037 707 Dihedral : 4.322 38.683 614 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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 (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: 1.21 (0.38), residues: 530 helix: 1.82 (0.27), residues: 369 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.001 0.001 HIS A 304 PHE 0.012 0.001 PHE A 22 TYR 0.019 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 1) link_NAG-ASN : angle 1.13750 ( 3) link_BETA1-4 : bond 0.00678 ( 1) link_BETA1-4 : angle 1.55594 ( 3) hydrogen bonds : bond 0.04302 ( 256) hydrogen bonds : angle 3.97523 ( 753) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.22738 ( 6) covalent geometry : bond 0.00270 ( 4193) covalent geometry : angle 0.50269 ( 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 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: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6350 (mm-30) REVERT: A 19 LYS cc_start: 0.8407 (mttt) cc_final: 0.7899 (mtmm) REVERT: A 27 LEU cc_start: 0.8241 (tt) cc_final: 0.8013 (tp) REVERT: A 488 MET cc_start: 0.6736 (mmm) cc_final: 0.6490 (mmm) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.2885 time to fit residues: 31.9379 Evaluate side-chains 84 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 Chi-restraints excluded: chain A residue 472 LEU 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: 0.6980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.198143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157884 restraints weight = 13518.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164754 restraints weight = 6085.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.169031 restraints weight = 3757.861| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4198 Z= 0.114 Angle : 0.501 7.123 5736 Z= 0.260 Chirality : 0.034 0.132 674 Planarity : 0.004 0.036 707 Dihedral : 4.182 37.395 614 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.36 % Allowed : 18.40 % 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: 1.26 (0.38), residues: 530 helix: 1.81 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.58 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 64 HIS 0.001 0.000 HIS A 367 PHE 0.011 0.001 PHE A 22 TYR 0.019 0.001 TYR A 240 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 1) link_NAG-ASN : angle 1.16824 ( 3) link_BETA1-4 : bond 0.00607 ( 1) link_BETA1-4 : angle 1.43758 ( 3) hydrogen bonds : bond 0.04207 ( 256) hydrogen bonds : angle 3.90898 ( 753) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.22480 ( 6) covalent geometry : bond 0.00249 ( 4193) covalent geometry : angle 0.49928 ( 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 87 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 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: symmetry clash REVERT: A 19 LYS cc_start: 0.8413 (mttt) cc_final: 0.7883 (mtmm) REVERT: A 27 LEU cc_start: 0.8238 (tt) cc_final: 0.8012 (tp) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.2601 time to fit residues: 28.0536 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 : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 CYS 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 Chi-restraints excluded: chain A residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 25 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.198721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.160519 restraints weight = 13482.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.166842 restraints weight = 6321.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170953 restraints weight = 3995.917| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4258 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= 0.111 Angle : 0.499 7.093 5736 Z= 0.258 Chirality : 0.033 0.128 674 Planarity : 0.004 0.037 707 Dihedral : 4.114 35.727 614 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 18.63 % Favored : 79.48 % 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: 1.25 (0.38), residues: 530 helix: 1.82 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.61 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.001 0.000 HIS A 367 PHE 0.012 0.001 PHE A 22 TYR 0.019 0.001 TYR A 240 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 1) link_NAG-ASN : angle 1.09936 ( 3) link_BETA1-4 : bond 0.00641 ( 1) link_BETA1-4 : angle 1.46353 ( 3) hydrogen bonds : bond 0.04066 ( 256) hydrogen bonds : angle 3.87198 ( 753) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.20815 ( 6) covalent geometry : bond 0.00245 ( 4193) covalent geometry : angle 0.49728 ( 5724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.69 seconds wall clock time: 53 minutes 59.67 seconds (3239.67 seconds total)