Starting phenix.real_space_refine on Thu Jul 24 02:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.map" model { file = "/net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zqi_11364/07_2025/6zqi_11364.cif" } resolution = 3.8 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3167 2.51 5 N 875 2.21 5 O 947 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.04, per 1000 atoms: 1.00 Number of scatterers: 5032 At special positions: 0 Unit cell: (74.36, 123.37, 138.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 947 8.00 N 875 7.00 C 3167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 67 " distance=2.04 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 NAG-ASN " NAG B 201 " - " ASN B 70 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1182 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 23.4% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.808A pdb=" N ALA A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.603A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.598A pdb=" N THR A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 396 " --> pdb=" O GLY A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 458 removed outlier: 5.797A pdb=" N SER A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.538A pdb=" N LEU A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.726A pdb=" N PHE A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.026A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.173A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.690A pdb=" N GLU A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.926A pdb=" N LYS A 291 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 removed outlier: 7.034A pdb=" N GLY A 127 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER A 58 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 125 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N CYS A 60 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS A 123 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 62 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N CYS A 121 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 274 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.641A pdb=" N ALA A 307 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.568A pdb=" N SER A 320 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.965A pdb=" N ARG A 358 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.199A pdb=" N TYR B 10 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 77 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N MET B 12 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY B 79 " --> pdb=" O MET B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 26 213 hydrogen bonds defined for protein. 576 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: 2.47 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1646 1.35 - 1.47: 1271 1.47 - 1.59: 2159 1.59 - 1.71: 0 1.71 - 1.83: 68 Bond restraints: 5144 Sorted by residual: bond pdb=" N ARG B 94 " pdb=" CA ARG B 94 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.30e+00 bond pdb=" N HIS A 250 " pdb=" CA HIS A 250 " ideal model delta sigma weight residual 1.455 1.482 -0.028 1.25e-02 6.40e+03 4.94e+00 bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" CE1 HIS A 250 " pdb=" NE2 HIS A 250 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.22e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.19e+00 ... (remaining 5139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 6902 2.47 - 4.93: 54 4.93 - 7.40: 4 7.40 - 9.86: 0 9.86 - 12.33: 2 Bond angle restraints: 6962 Sorted by residual: angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 126.73 -12.33 2.30e+00 1.89e-01 2.87e+01 angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 125.70 -11.30 2.30e+00 1.89e-01 2.41e+01 angle pdb=" N CYS A 116 " pdb=" CA CYS A 116 " pdb=" C CYS A 116 " ideal model delta sigma weight residual 109.52 114.59 -5.07 1.55e+00 4.16e-01 1.07e+01 angle pdb=" C SER B 71 " pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 122.32 127.75 -5.43 1.76e+00 3.23e-01 9.52e+00 angle pdb=" C LYS A 444 " pdb=" N PHE A 445 " pdb=" CA PHE A 445 " ideal model delta sigma weight residual 120.68 116.13 4.55 1.70e+00 3.46e-01 7.16e+00 ... (remaining 6957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2817 17.87 - 35.75: 189 35.75 - 53.62: 39 53.62 - 71.50: 6 71.50 - 89.37: 5 Dihedral angle restraints: 3056 sinusoidal: 1203 harmonic: 1853 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 -179.58 -87.42 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual -86.00 -23.78 -62.22 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CB CYS B 34 " pdb=" SG CYS B 34 " pdb=" SG CYS B 69 " pdb=" CB CYS B 69 " ideal model delta sinusoidal sigma weight residual -86.00 -28.93 -57.07 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 3053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 602 0.048 - 0.097: 137 0.097 - 0.145: 30 0.145 - 0.193: 3 0.193 - 0.241: 1 Chirality restraints: 773 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA CYS A 92 " pdb=" N CYS A 92 " pdb=" C CYS A 92 " pdb=" CB CYS A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ARG B 94 " pdb=" N ARG B 94 " pdb=" C ARG B 94 " pdb=" CB ARG B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 770 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 74 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A 75 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 45 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO B 46 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 53 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO B 54 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.014 5.00e-02 4.00e+02 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1744 2.85 - 3.36: 4336 3.36 - 3.87: 7621 3.87 - 4.39: 8126 4.39 - 4.90: 14511 Nonbonded interactions: 36338 Sorted by model distance: nonbonded pdb=" OD1 ASP A 380 " pdb=" NH1 ARG A 403 " model vdw 2.336 3.120 nonbonded pdb=" OG1 THR A 322 " pdb=" OG1 THR A 326 " model vdw 2.361 3.040 nonbonded pdb=" O ILE A 497 " pdb=" OG1 THR A 501 " model vdw 2.370 3.040 nonbonded pdb=" OE1 GLU A 178 " pdb=" OG SER A 188 " model vdw 2.385 3.040 nonbonded pdb=" O SER A 369 " pdb=" OG SER A 369 " model vdw 2.389 3.040 ... (remaining 36333 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: 42.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.810 Find NCS groups from input model: 0.070 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:4.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.002 0.031 5154 Z= 0.133 Angle : 0.586 12.331 6983 Z= 0.333 Chirality : 0.044 0.241 773 Planarity : 0.003 0.032 887 Dihedral : 12.439 89.370 1847 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.12 % Allowed : 3.72 % Favored : 95.16 % 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: -2.14 (0.29), residues: 649 helix: -0.02 (0.42), residues: 132 sheet: -0.56 (0.35), residues: 197 loop : -2.67 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.002 0.000 HIS A 160 PHE 0.017 0.001 PHE A 445 TYR 0.010 0.001 TYR A 61 ARG 0.003 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00635 ( 1) link_NAG-ASN : angle 1.64114 ( 3) hydrogen bonds : bond 0.12500 ( 203) hydrogen bonds : angle 5.23775 ( 576) SS BOND : bond 0.00503 ( 9) SS BOND : angle 3.08629 ( 18) covalent geometry : bond 0.00242 ( 5144) covalent geometry : angle 0.56453 ( 6962) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 189 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7547 (mtm) cc_final: 0.7152 (mtm) REVERT: A 77 GLN cc_start: 0.8105 (tp40) cc_final: 0.7776 (mt0) REVERT: A 81 TYR cc_start: 0.8482 (t80) cc_final: 0.8174 (t80) REVERT: A 178 GLU cc_start: 0.7788 (tp30) cc_final: 0.7464 (mm-30) REVERT: A 201 ASP cc_start: 0.8099 (t0) cc_final: 0.7829 (t0) REVERT: A 209 ASN cc_start: 0.8389 (t0) cc_final: 0.8050 (t0) REVERT: A 221 ASP cc_start: 0.7948 (t70) cc_final: 0.7688 (t0) REVERT: A 330 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 374 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8178 (mmtm) REVERT: A 422 MET cc_start: 0.8617 (tpp) cc_final: 0.8021 (tpp) REVERT: A 432 PHE cc_start: 0.7640 (m-10) cc_final: 0.4941 (p90) REVERT: A 447 HIS cc_start: 0.8448 (t-90) cc_final: 0.7942 (t-170) REVERT: A 455 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7000 (mptt) REVERT: A 471 PHE cc_start: 0.8609 (m-10) cc_final: 0.7968 (t80) REVERT: B 32 ASN cc_start: 0.6953 (t0) cc_final: 0.6699 (t0) REVERT: B 39 MET cc_start: 0.7032 (ptt) cc_final: 0.6826 (ttt) REVERT: B 101 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7546 (m-70) REVERT: C 127 GLU cc_start: 0.8549 (tt0) cc_final: 0.8067 (mt-10) outliers start: 6 outliers final: 1 residues processed: 192 average time/residue: 0.4231 time to fit residues: 98.5910 Evaluate side-chains 150 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain B residue 101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 363 ASN C 133 ASN C 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133257 restraints weight = 7363.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137682 restraints weight = 4261.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140839 restraints weight = 2988.920| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5154 Z= 0.142 Angle : 0.666 14.907 6983 Z= 0.341 Chirality : 0.046 0.286 773 Planarity : 0.004 0.033 887 Dihedral : 5.777 78.031 726 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.10 % Allowed : 15.08 % Favored : 80.82 % 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 (0.31), residues: 649 helix: 1.28 (0.46), residues: 131 sheet: -0.23 (0.36), residues: 195 loop : -2.20 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 129 HIS 0.006 0.001 HIS A 27 PHE 0.009 0.001 PHE A 219 TYR 0.012 0.001 TYR A 61 ARG 0.006 0.001 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 1) link_NAG-ASN : angle 2.20115 ( 3) hydrogen bonds : bond 0.03577 ( 203) hydrogen bonds : angle 4.42174 ( 576) SS BOND : bond 0.00598 ( 9) SS BOND : angle 3.52976 ( 18) covalent geometry : bond 0.00325 ( 5144) covalent geometry : angle 0.64094 ( 6962) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8320 (tp40) cc_final: 0.8066 (mt0) REVERT: A 81 TYR cc_start: 0.8585 (t80) cc_final: 0.8208 (t80) REVERT: A 178 GLU cc_start: 0.8191 (tp30) cc_final: 0.7483 (mm-30) REVERT: A 201 ASP cc_start: 0.8196 (t0) cc_final: 0.7942 (t0) REVERT: A 203 TYR cc_start: 0.8375 (m-10) cc_final: 0.7954 (m-80) REVERT: A 221 ASP cc_start: 0.8157 (t70) cc_final: 0.7868 (t0) REVERT: A 241 GLU cc_start: 0.7983 (mp0) cc_final: 0.7754 (mp0) REVERT: A 301 LEU cc_start: 0.8104 (mt) cc_final: 0.7831 (mp) REVERT: A 365 VAL cc_start: 0.9147 (p) cc_final: 0.8881 (p) REVERT: A 422 MET cc_start: 0.8680 (tpp) cc_final: 0.8048 (tpp) REVERT: A 432 PHE cc_start: 0.7725 (m-10) cc_final: 0.4980 (p90) REVERT: A 447 HIS cc_start: 0.8563 (t-90) cc_final: 0.8126 (t-170) REVERT: A 455 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7295 (mptt) REVERT: A 466 GLN cc_start: 0.8892 (mp10) cc_final: 0.8076 (pm20) REVERT: A 471 PHE cc_start: 0.8561 (m-10) cc_final: 0.7971 (t80) REVERT: B 32 ASN cc_start: 0.6904 (t0) cc_final: 0.6524 (t0) REVERT: B 39 MET cc_start: 0.7050 (ptt) cc_final: 0.6830 (ttt) REVERT: C 127 GLU cc_start: 0.8520 (tt0) cc_final: 0.8246 (mt-10) outliers start: 22 outliers final: 14 residues processed: 172 average time/residue: 0.2663 time to fit residues: 60.0069 Evaluate side-chains 160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.0050 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131324 restraints weight = 7495.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135704 restraints weight = 4351.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138880 restraints weight = 3056.589| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5154 Z= 0.147 Angle : 0.669 18.318 6983 Z= 0.343 Chirality : 0.046 0.310 773 Planarity : 0.004 0.036 887 Dihedral : 5.577 79.562 724 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.72 % Allowed : 20.67 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.32), residues: 649 helix: 1.58 (0.46), residues: 132 sheet: -0.18 (0.36), residues: 197 loop : -1.91 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.022 0.001 PHE A 454 TYR 0.013 0.001 TYR A 61 ARG 0.003 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 1) link_NAG-ASN : angle 1.80582 ( 3) hydrogen bonds : bond 0.03521 ( 203) hydrogen bonds : angle 4.22931 ( 576) SS BOND : bond 0.00659 ( 9) SS BOND : angle 3.67818 ( 18) covalent geometry : bond 0.00339 ( 5144) covalent geometry : angle 0.64251 ( 6962) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.196 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8615 (t80) cc_final: 0.8239 (t80) REVERT: A 178 GLU cc_start: 0.8223 (tp30) cc_final: 0.7513 (mm-30) REVERT: A 192 GLU cc_start: 0.8115 (mp0) cc_final: 0.7882 (mp0) REVERT: A 201 ASP cc_start: 0.8221 (t0) cc_final: 0.7943 (t0) REVERT: A 203 TYR cc_start: 0.8389 (m-10) cc_final: 0.8110 (m-80) REVERT: A 221 ASP cc_start: 0.8151 (t70) cc_final: 0.7877 (t0) REVERT: A 241 GLU cc_start: 0.8021 (mp0) cc_final: 0.7759 (mp0) REVERT: A 285 ILE cc_start: 0.8857 (mp) cc_final: 0.8640 (mt) REVERT: A 301 LEU cc_start: 0.7948 (mt) cc_final: 0.7691 (mp) REVERT: A 422 MET cc_start: 0.8567 (tpp) cc_final: 0.7948 (tpp) REVERT: A 432 PHE cc_start: 0.7862 (m-10) cc_final: 0.4958 (p90) REVERT: A 438 MET cc_start: 0.6387 (mpp) cc_final: 0.6037 (mpp) REVERT: A 447 HIS cc_start: 0.8681 (t-90) cc_final: 0.8151 (t-170) REVERT: A 455 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7386 (mptt) REVERT: A 471 PHE cc_start: 0.8574 (m-10) cc_final: 0.8033 (t80) REVERT: B 32 ASN cc_start: 0.6929 (t0) cc_final: 0.6503 (t0) REVERT: C 127 GLU cc_start: 0.8387 (tt0) cc_final: 0.8120 (mt-10) outliers start: 20 outliers final: 15 residues processed: 166 average time/residue: 0.3288 time to fit residues: 73.1909 Evaluate side-chains 161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** B 59 GLN ** 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 = 0.3903 r_free = 0.3903 target = 0.160288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.130266 restraints weight = 7547.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.134593 restraints weight = 4311.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137592 restraints weight = 2972.974| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5154 Z= 0.162 Angle : 0.671 13.895 6983 Z= 0.345 Chirality : 0.045 0.242 773 Planarity : 0.004 0.037 887 Dihedral : 5.687 79.415 724 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.21 % Allowed : 21.97 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.74 (0.32), residues: 649 helix: 1.75 (0.47), residues: 132 sheet: -0.11 (0.37), residues: 196 loop : -1.77 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.016 0.001 PHE A 454 TYR 0.015 0.002 TYR A 61 ARG 0.003 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00683 ( 1) link_NAG-ASN : angle 1.84113 ( 3) hydrogen bonds : bond 0.03626 ( 203) hydrogen bonds : angle 4.28564 ( 576) SS BOND : bond 0.00400 ( 9) SS BOND : angle 3.69138 ( 18) covalent geometry : bond 0.00371 ( 5144) covalent geometry : angle 0.64389 ( 6962) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8705 (t80) cc_final: 0.8345 (t80) REVERT: A 178 GLU cc_start: 0.8060 (tp30) cc_final: 0.7450 (mm-30) REVERT: A 192 GLU cc_start: 0.8101 (mp0) cc_final: 0.7232 (mp0) REVERT: A 201 ASP cc_start: 0.8241 (t0) cc_final: 0.7990 (t0) REVERT: A 221 ASP cc_start: 0.8190 (t70) cc_final: 0.7909 (t0) REVERT: A 241 GLU cc_start: 0.8166 (mp0) cc_final: 0.7840 (mp0) REVERT: A 301 LEU cc_start: 0.8055 (mt) cc_final: 0.7529 (mp) REVERT: A 332 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7518 (tt0) REVERT: A 422 MET cc_start: 0.8569 (tpp) cc_final: 0.7968 (tpp) REVERT: A 438 MET cc_start: 0.6493 (mpp) cc_final: 0.6067 (mpp) REVERT: A 447 HIS cc_start: 0.8767 (t-90) cc_final: 0.8235 (t-170) REVERT: A 455 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7248 (mptt) REVERT: A 466 GLN cc_start: 0.8977 (mp10) cc_final: 0.8694 (pm20) REVERT: A 471 PHE cc_start: 0.8578 (m-10) cc_final: 0.7990 (t80) REVERT: B 25 PHE cc_start: 0.7352 (p90) cc_final: 0.7065 (p90) REVERT: B 32 ASN cc_start: 0.6738 (t0) cc_final: 0.6490 (t0) outliers start: 28 outliers final: 22 residues processed: 168 average time/residue: 0.2631 time to fit residues: 56.3876 Evaluate side-chains 163 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 62 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 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 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 = 0.3908 r_free = 0.3908 target = 0.160491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.129212 restraints weight = 7426.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133581 restraints weight = 4361.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136394 restraints weight = 3068.030| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5154 Z= 0.130 Angle : 0.676 21.313 6983 Z= 0.348 Chirality : 0.046 0.315 773 Planarity : 0.004 0.037 887 Dihedral : 5.549 80.067 724 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.03 % Allowed : 23.09 % Favored : 71.88 % 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: -0.60 (0.32), residues: 649 helix: 2.05 (0.48), residues: 131 sheet: 0.06 (0.37), residues: 196 loop : -1.81 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.023 0.001 PHE A 498 TYR 0.019 0.002 TYR B 60 ARG 0.003 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 1) link_NAG-ASN : angle 1.87373 ( 3) hydrogen bonds : bond 0.03402 ( 203) hydrogen bonds : angle 4.12897 ( 576) SS BOND : bond 0.00750 ( 9) SS BOND : angle 3.72373 ( 18) covalent geometry : bond 0.00293 ( 5144) covalent geometry : angle 0.64866 ( 6962) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8722 (t80) cc_final: 0.8365 (t80) REVERT: A 178 GLU cc_start: 0.8093 (tp30) cc_final: 0.7489 (mm-30) REVERT: A 192 GLU cc_start: 0.8125 (mp0) cc_final: 0.7213 (mp0) REVERT: A 201 ASP cc_start: 0.8399 (t0) cc_final: 0.7997 (t0) REVERT: A 221 ASP cc_start: 0.8205 (t70) cc_final: 0.7908 (t0) REVERT: A 241 GLU cc_start: 0.8150 (mp0) cc_final: 0.7803 (mp0) REVERT: A 332 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7645 (tt0) REVERT: A 422 MET cc_start: 0.8515 (tpp) cc_final: 0.7989 (tpp) REVERT: A 447 HIS cc_start: 0.8803 (t-90) cc_final: 0.8133 (t-170) REVERT: A 455 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7235 (mptt) REVERT: A 466 GLN cc_start: 0.8916 (mp10) cc_final: 0.8649 (pm20) REVERT: A 471 PHE cc_start: 0.8654 (m-10) cc_final: 0.8040 (t80) REVERT: B 32 ASN cc_start: 0.6671 (t0) cc_final: 0.6462 (t0) REVERT: C 161 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8252 (mm) outliers start: 27 outliers final: 18 residues processed: 167 average time/residue: 0.2240 time to fit residues: 47.8524 Evaluate side-chains 161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 227 HIS ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121515 restraints weight = 7665.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125503 restraints weight = 4554.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128352 restraints weight = 3256.497| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 5154 Z= 0.290 Angle : 0.804 16.461 6983 Z= 0.419 Chirality : 0.049 0.298 773 Planarity : 0.005 0.041 887 Dihedral : 6.169 78.749 724 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.03 % Allowed : 23.84 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.31), residues: 649 helix: 1.14 (0.44), residues: 136 sheet: -0.11 (0.37), residues: 197 loop : -1.92 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 129 HIS 0.007 0.001 HIS A 211 PHE 0.026 0.002 PHE A 454 TYR 0.026 0.003 TYR A 61 ARG 0.004 0.001 ARG A 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 1) link_NAG-ASN : angle 1.70532 ( 3) hydrogen bonds : bond 0.04615 ( 203) hydrogen bonds : angle 4.69201 ( 576) SS BOND : bond 0.00725 ( 9) SS BOND : angle 4.04561 ( 18) covalent geometry : bond 0.00669 ( 5144) covalent geometry : angle 0.77723 ( 6962) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 81 TYR cc_start: 0.8449 (t80) cc_final: 0.7944 (t80) REVERT: A 192 GLU cc_start: 0.8344 (mp0) cc_final: 0.7521 (mp0) REVERT: A 201 ASP cc_start: 0.8425 (t0) cc_final: 0.8091 (t0) REVERT: A 221 ASP cc_start: 0.8318 (t70) cc_final: 0.8020 (t0) REVERT: A 332 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 422 MET cc_start: 0.8651 (tpp) cc_final: 0.8202 (tpp) REVERT: A 471 PHE cc_start: 0.8767 (m-10) cc_final: 0.8075 (t80) REVERT: B 32 ASN cc_start: 0.7077 (t0) cc_final: 0.6761 (t0) REVERT: B 34 CYS cc_start: 0.7152 (t) cc_final: 0.6679 (t) REVERT: C 161 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7667 (mm) outliers start: 27 outliers final: 21 residues processed: 158 average time/residue: 0.1884 time to fit residues: 38.6160 Evaluate side-chains 153 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 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 = 0.3883 r_free = 0.3883 target = 0.157714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126950 restraints weight = 7365.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131237 restraints weight = 4276.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134186 restraints weight = 2997.226| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5154 Z= 0.134 Angle : 0.740 23.755 6983 Z= 0.375 Chirality : 0.047 0.324 773 Planarity : 0.004 0.039 887 Dihedral : 5.807 80.845 724 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.84 % Allowed : 25.70 % Favored : 69.46 % 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: -0.67 (0.32), residues: 649 helix: 1.81 (0.46), residues: 131 sheet: 0.02 (0.38), residues: 185 loop : -1.73 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.020 0.001 PHE A 454 TYR 0.011 0.001 TYR A 61 ARG 0.002 0.000 ARG B 90 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 1) link_NAG-ASN : angle 2.05342 ( 3) hydrogen bonds : bond 0.03695 ( 203) hydrogen bonds : angle 4.27844 ( 576) SS BOND : bond 0.00947 ( 9) SS BOND : angle 3.98341 ( 18) covalent geometry : bond 0.00298 ( 5144) covalent geometry : angle 0.71205 ( 6962) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8193 (mm-40) REVERT: A 178 GLU cc_start: 0.8040 (tp30) cc_final: 0.7517 (mm-30) REVERT: A 192 GLU cc_start: 0.8245 (mp0) cc_final: 0.7437 (mp0) REVERT: A 201 ASP cc_start: 0.8406 (t0) cc_final: 0.8084 (t0) REVERT: A 221 ASP cc_start: 0.8271 (t70) cc_final: 0.8057 (t0) REVERT: A 368 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: A 422 MET cc_start: 0.8576 (tpp) cc_final: 0.8118 (tpp) REVERT: A 455 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7209 (mptt) REVERT: A 466 GLN cc_start: 0.8874 (mp10) cc_final: 0.8648 (pm20) REVERT: A 468 LEU cc_start: 0.8567 (mt) cc_final: 0.8281 (mm) REVERT: A 471 PHE cc_start: 0.8768 (m-10) cc_final: 0.8079 (t80) REVERT: B 32 ASN cc_start: 0.6925 (t0) cc_final: 0.6624 (t0) REVERT: B 60 TYR cc_start: 0.8981 (m-80) cc_final: 0.8708 (m-80) REVERT: C 161 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7892 (mm) outliers start: 26 outliers final: 20 residues processed: 155 average time/residue: 0.2008 time to fit residues: 41.1033 Evaluate side-chains 155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** B 59 GLN ** 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 = 0.3898 r_free = 0.3898 target = 0.159672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128911 restraints weight = 7511.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133231 restraints weight = 4344.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136227 restraints weight = 3037.006| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5154 Z= 0.134 Angle : 0.710 18.539 6983 Z= 0.365 Chirality : 0.047 0.300 773 Planarity : 0.004 0.038 887 Dihedral : 5.637 80.891 724 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.91 % Allowed : 27.00 % Favored : 69.09 % 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: -0.47 (0.32), residues: 649 helix: 2.06 (0.46), residues: 131 sheet: 0.17 (0.38), residues: 190 loop : -1.67 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 129 HIS 0.005 0.001 HIS A 27 PHE 0.018 0.001 PHE A 454 TYR 0.019 0.001 TYR A 203 ARG 0.002 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 1) link_NAG-ASN : angle 1.67568 ( 3) hydrogen bonds : bond 0.03583 ( 203) hydrogen bonds : angle 4.10606 ( 576) SS BOND : bond 0.00614 ( 9) SS BOND : angle 3.98665 ( 18) covalent geometry : bond 0.00305 ( 5144) covalent geometry : angle 0.68031 ( 6962) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8218 (mm-40) REVERT: A 178 GLU cc_start: 0.8090 (tp30) cc_final: 0.7560 (mm-30) REVERT: A 192 GLU cc_start: 0.8260 (mp0) cc_final: 0.7404 (mp0) REVERT: A 201 ASP cc_start: 0.8558 (t0) cc_final: 0.8150 (t0) REVERT: A 203 TYR cc_start: 0.8499 (m-80) cc_final: 0.8027 (m-80) REVERT: A 350 THR cc_start: 0.9280 (p) cc_final: 0.9003 (t) REVERT: A 368 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 422 MET cc_start: 0.8500 (tpp) cc_final: 0.8000 (tpp) REVERT: A 455 LYS cc_start: 0.7686 (ttmt) cc_final: 0.6923 (mptt) REVERT: A 468 LEU cc_start: 0.8551 (mt) cc_final: 0.8267 (mm) REVERT: A 471 PHE cc_start: 0.8795 (m-10) cc_final: 0.8092 (t80) REVERT: B 32 ASN cc_start: 0.6555 (t0) cc_final: 0.6329 (t0) REVERT: B 60 TYR cc_start: 0.8987 (m-80) cc_final: 0.8687 (m-80) REVERT: C 161 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8196 (mm) outliers start: 21 outliers final: 18 residues processed: 150 average time/residue: 0.1910 time to fit residues: 38.0638 Evaluate side-chains 151 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.160683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130474 restraints weight = 7399.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134644 restraints weight = 4428.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137549 restraints weight = 3128.940| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5154 Z= 0.126 Angle : 0.744 19.408 6983 Z= 0.374 Chirality : 0.047 0.310 773 Planarity : 0.004 0.038 887 Dihedral : 5.558 81.478 724 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.91 % Allowed : 27.93 % Favored : 68.16 % 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: -0.31 (0.33), residues: 649 helix: 2.31 (0.47), residues: 131 sheet: 0.30 (0.38), residues: 190 loop : -1.66 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 129 HIS 0.005 0.001 HIS A 160 PHE 0.016 0.001 PHE A 454 TYR 0.016 0.001 TYR A 203 ARG 0.002 0.000 ARG C 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 1) link_NAG-ASN : angle 1.69258 ( 3) hydrogen bonds : bond 0.03515 ( 203) hydrogen bonds : angle 4.01281 ( 576) SS BOND : bond 0.00751 ( 9) SS BOND : angle 3.99154 ( 18) covalent geometry : bond 0.00284 ( 5144) covalent geometry : angle 0.71568 ( 6962) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8194 (mm-40) REVERT: A 178 GLU cc_start: 0.8071 (tp30) cc_final: 0.7493 (tp30) REVERT: A 192 GLU cc_start: 0.8228 (mp0) cc_final: 0.7375 (mp0) REVERT: A 201 ASP cc_start: 0.8584 (t0) cc_final: 0.8148 (t0) REVERT: A 332 GLN cc_start: 0.7106 (tt0) cc_final: 0.6700 (tm-30) REVERT: A 368 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: A 422 MET cc_start: 0.8501 (tpp) cc_final: 0.7938 (tpp) REVERT: A 455 LYS cc_start: 0.7663 (ttmt) cc_final: 0.6933 (mptt) REVERT: A 468 LEU cc_start: 0.8526 (mt) cc_final: 0.8273 (mm) REVERT: A 471 PHE cc_start: 0.8713 (m-10) cc_final: 0.8001 (t80) REVERT: B 32 ASN cc_start: 0.6434 (t0) cc_final: 0.6207 (t0) REVERT: B 60 TYR cc_start: 0.8995 (m-80) cc_final: 0.8739 (m-80) REVERT: C 161 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8169 (mm) outliers start: 21 outliers final: 19 residues processed: 155 average time/residue: 0.1460 time to fit residues: 29.6675 Evaluate side-chains 156 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 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 = 0.3912 r_free = 0.3912 target = 0.161167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130290 restraints weight = 7435.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134585 restraints weight = 4328.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137592 restraints weight = 3028.099| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5154 Z= 0.126 Angle : 0.722 17.603 6983 Z= 0.368 Chirality : 0.046 0.282 773 Planarity : 0.004 0.037 887 Dihedral : 5.517 80.895 724 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.47 % Allowed : 27.75 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.33), residues: 649 helix: 2.24 (0.46), residues: 132 sheet: 0.33 (0.38), residues: 190 loop : -1.61 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 129 HIS 0.004 0.001 HIS A 27 PHE 0.017 0.001 PHE A 454 TYR 0.025 0.001 TYR A 203 ARG 0.008 0.000 ARG B 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 1) link_NAG-ASN : angle 1.51041 ( 3) hydrogen bonds : bond 0.03418 ( 203) hydrogen bonds : angle 3.95558 ( 576) SS BOND : bond 0.00674 ( 9) SS BOND : angle 3.91403 ( 18) covalent geometry : bond 0.00282 ( 5144) covalent geometry : angle 0.69412 ( 6962) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 178 GLU cc_start: 0.8042 (tp30) cc_final: 0.7507 (tp30) REVERT: A 192 GLU cc_start: 0.8224 (mp0) cc_final: 0.7384 (mp0) REVERT: A 201 ASP cc_start: 0.8657 (t0) cc_final: 0.8095 (t0) REVERT: A 332 GLN cc_start: 0.6950 (tt0) cc_final: 0.6499 (tm-30) REVERT: A 368 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: A 422 MET cc_start: 0.8330 (tpp) cc_final: 0.7638 (tpp) REVERT: A 455 LYS cc_start: 0.7779 (ttmt) cc_final: 0.6980 (mmtm) REVERT: A 468 LEU cc_start: 0.8961 (mt) cc_final: 0.8751 (mm) REVERT: A 471 PHE cc_start: 0.8641 (m-10) cc_final: 0.7932 (t80) REVERT: B 32 ASN cc_start: 0.6412 (t0) cc_final: 0.6175 (t0) REVERT: B 60 TYR cc_start: 0.8994 (m-80) cc_final: 0.8662 (m-10) REVERT: B 101 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.7333 (m-70) REVERT: C 161 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8068 (mm) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 0.1956 time to fit residues: 39.3241 Evaluate side-chains 157 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 445 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS ** B 59 GLN ** 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 = 0.3905 r_free = 0.3905 target = 0.159775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.128514 restraints weight = 7531.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.132935 restraints weight = 4388.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136026 restraints weight = 3060.270| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5154 Z= 0.130 Angle : 0.726 18.568 6983 Z= 0.368 Chirality : 0.046 0.295 773 Planarity : 0.004 0.037 887 Dihedral : 5.480 80.469 724 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.91 % Allowed : 28.49 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.33), residues: 649 helix: 2.28 (0.47), residues: 132 sheet: 0.36 (0.38), residues: 190 loop : -1.59 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 129 HIS 0.004 0.001 HIS A 27 PHE 0.016 0.001 PHE A 454 TYR 0.017 0.001 TYR A 306 ARG 0.003 0.000 ARG B 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00437 ( 1) link_NAG-ASN : angle 1.49277 ( 3) hydrogen bonds : bond 0.03460 ( 203) hydrogen bonds : angle 3.94808 ( 576) SS BOND : bond 0.00714 ( 9) SS BOND : angle 3.91127 ( 18) covalent geometry : bond 0.00294 ( 5144) covalent geometry : angle 0.69912 ( 6962) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.31 seconds wall clock time: 64 minutes 26.11 seconds (3866.11 seconds total)