Starting phenix.real_space_refine on Sun Apr 27 15:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.map" model { file = "/net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ykh_39372/04_2025/8ykh_39372.cif" } resolution = 3.27 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3302 atoms to isotropic. 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 14 5.16 5 C 2114 2.51 5 N 557 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1761 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain breaks: 1 Chain: "C" 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: 3.56, per 1000 atoms: 1.07 Number of scatterers: 3330 At special positions: 0 Unit cell: (82.1642, 71.611, 84.4256, 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 14 16.00 O 645 8.00 N 557 7.00 C 2114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 400.1 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.3% alpha, 34.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 186 through 190 removed outlier: 3.651A pdb=" N LYS A 189 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A 190 " --> pdb=" O THR A 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 186 through 190' Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.578A pdb=" N THR A 215 " --> pdb=" O PRO A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.734A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.871A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.550A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.835A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.620A pdb=" N ASP A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 12 removed outlier: 4.030A pdb=" N LEU A 10 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU A 104 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A 12 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.504A pdb=" N PHE A 203 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.977A pdb=" N VAL A 133 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ALA A 155 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TYR A 175 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP A 157 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG A 173 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TRP A 159 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 132 through 133 removed outlier: 3.977A pdb=" N VAL A 133 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE A 224 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A 231 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.502A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 108 hydrogen bonds defined for protein. 252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1060 1.34 - 1.46: 917 1.46 - 1.59: 1421 1.59 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3414 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" CA TYR B 396 " pdb=" CB TYR B 396 " ideal model delta sigma weight residual 1.535 1.512 0.022 2.02e-02 2.45e+03 1.23e+00 bond pdb=" CA GLY A 98 " pdb=" C GLY A 98 " ideal model delta sigma weight residual 1.519 1.509 0.009 8.90e-03 1.26e+04 1.14e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.07e+00 ... (remaining 3409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 4425 1.33 - 2.65: 176 2.65 - 3.98: 32 3.98 - 5.31: 7 5.31 - 6.63: 4 Bond angle restraints: 4644 Sorted by residual: angle pdb=" CB LYS A 134 " pdb=" CG LYS A 134 " pdb=" CD LYS A 134 " ideal model delta sigma weight residual 111.30 117.93 -6.63 2.30e+00 1.89e-01 8.32e+00 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 120.26 -5.86 2.30e+00 1.89e-01 6.48e+00 angle pdb=" CA LYS A 134 " pdb=" CB LYS A 134 " pdb=" CG LYS A 134 " ideal model delta sigma weight residual 114.10 119.12 -5.02 2.00e+00 2.50e-01 6.29e+00 angle pdb=" C GLY A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.81e+00 angle pdb=" C VAL A 133 " pdb=" N LYS A 134 " pdb=" CA LYS A 134 " ideal model delta sigma weight residual 120.67 123.56 -2.89 1.34e+00 5.57e-01 4.64e+00 ... (remaining 4639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 1884 17.63 - 35.25: 131 35.25 - 52.88: 13 52.88 - 70.50: 5 70.50 - 88.13: 3 Dihedral angle restraints: 2036 sinusoidal: 810 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 63.21 29.79 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CG ARG A 166 " pdb=" CD ARG A 166 " pdb=" NE ARG A 166 " pdb=" CZ ARG A 166 " ideal model delta sinusoidal sigma weight residual 90.00 130.22 -40.22 2 1.50e+01 4.44e-03 8.89e+00 dihedral pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " ideal model delta sinusoidal sigma weight residual -90.00 -49.81 -40.19 2 1.50e+01 4.44e-03 8.88e+00 ... (remaining 2033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 298 0.033 - 0.066: 135 0.066 - 0.099: 48 0.099 - 0.131: 23 0.131 - 0.164: 4 Chirality restraints: 508 Sorted by residual: chirality pdb=" CB VAL A 188 " pdb=" CA VAL A 188 " pdb=" CG1 VAL A 188 " pdb=" CG2 VAL A 188 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE A 145 " pdb=" N ILE A 145 " pdb=" C ILE A 145 " pdb=" CB ILE A 145 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 505 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 134 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 135 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 79 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 80 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 81 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" CD GLU A 81 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU A 81 " 0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 81 " 0.007 2.00e-02 2.50e+03 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 896 2.80 - 3.32: 2859 3.32 - 3.85: 4973 3.85 - 4.37: 5882 4.37 - 4.90: 10391 Nonbonded interactions: 25001 Sorted by model distance: nonbonded pdb=" NE ARG A 177 " pdb=" OE2 GLU B 484 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.311 3.120 nonbonded pdb=" OG SER A 93 " pdb=" OD1 ASN B 487 " model vdw 2.374 3.040 nonbonded pdb=" O SER A 121 " pdb=" NE2 GLN A 124 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.385 3.040 ... (remaining 24996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.080 Find NCS groups from input model: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3422 Z= 0.203 Angle : 0.650 6.634 4662 Z= 0.338 Chirality : 0.046 0.164 508 Planarity : 0.005 0.045 597 Dihedral : 12.008 88.131 1240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.85 (0.40), residues: 417 helix: -3.35 (1.00), residues: 20 sheet: 0.37 (0.46), residues: 142 loop : -0.88 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.014 0.001 PHE B 347 TYR 0.014 0.001 TYR B 473 ARG 0.006 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 1) link_NAG-ASN : angle 1.55952 ( 3) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 3.73129 ( 3) hydrogen bonds : bond 0.18192 ( 96) hydrogen bonds : angle 6.84699 ( 252) SS BOND : bond 0.00528 ( 6) SS BOND : angle 1.06416 ( 12) covalent geometry : bond 0.00465 ( 3414) covalent geometry : angle 0.64080 ( 4644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8550 (mm) cc_final: 0.8340 (mm) REVERT: A 214 ASP cc_start: 0.8321 (m-30) cc_final: 0.7827 (m-30) REVERT: B 386 LYS cc_start: 0.8560 (mtmt) cc_final: 0.7900 (ttpt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2564 time to fit residues: 16.5659 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 0.0470 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0570 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.064954 restraints weight = 7093.976| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.87 r_work: 0.2755 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3422 Z= 0.111 Angle : 0.594 6.033 4662 Z= 0.302 Chirality : 0.045 0.145 508 Planarity : 0.004 0.048 597 Dihedral : 5.722 54.452 510 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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: -0.65 (0.41), residues: 417 helix: -2.69 (0.96), residues: 21 sheet: 0.71 (0.47), residues: 137 loop : -0.90 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS A 206 PHE 0.009 0.001 PHE A 203 TYR 0.009 0.001 TYR A 181 ARG 0.003 0.000 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 1) link_NAG-ASN : angle 0.88722 ( 3) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 2.60900 ( 3) hydrogen bonds : bond 0.03650 ( 96) hydrogen bonds : angle 5.28796 ( 252) SS BOND : bond 0.00442 ( 6) SS BOND : angle 0.85867 ( 12) covalent geometry : bond 0.00254 ( 3414) covalent geometry : angle 0.58891 ( 4644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7973 (tp30) cc_final: 0.7664 (tp30) REVERT: A 102 LYS cc_start: 0.8824 (tptp) cc_final: 0.8617 (tptp) REVERT: A 169 GLU cc_start: 0.8474 (tt0) cc_final: 0.7872 (tt0) REVERT: A 214 ASP cc_start: 0.8616 (m-30) cc_final: 0.8184 (m-30) REVERT: B 386 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8037 (ttpt) REVERT: B 444 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8330 (mtmm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2734 time to fit residues: 19.0468 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 158 ASN A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066453 restraints weight = 6901.149| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.63 r_work: 0.2810 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3422 Z= 0.099 Angle : 0.557 6.009 4662 Z= 0.283 Chirality : 0.045 0.143 508 Planarity : 0.004 0.048 597 Dihedral : 5.522 54.486 510 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.28 % Allowed : 9.94 % Favored : 89.78 % 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: -0.63 (0.41), residues: 417 helix: -3.16 (0.78), residues: 27 sheet: 0.86 (0.48), residues: 137 loop : -0.85 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 206 PHE 0.010 0.001 PHE A 203 TYR 0.005 0.001 TYR A 175 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 1) link_NAG-ASN : angle 0.82015 ( 3) link_BETA1-4 : bond 0.00427 ( 1) link_BETA1-4 : angle 2.46066 ( 3) hydrogen bonds : bond 0.03207 ( 96) hydrogen bonds : angle 5.00705 ( 252) SS BOND : bond 0.00356 ( 6) SS BOND : angle 0.72470 ( 12) covalent geometry : bond 0.00225 ( 3414) covalent geometry : angle 0.55331 ( 4644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7882 (tp30) cc_final: 0.7623 (tp30) REVERT: A 169 GLU cc_start: 0.8412 (tt0) cc_final: 0.7922 (tt0) REVERT: A 214 ASP cc_start: 0.8509 (m-30) cc_final: 0.8180 (m-30) REVERT: B 386 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8139 (ttpt) REVERT: B 444 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8644 (mtmt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.3128 time to fit residues: 20.1826 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.063985 restraints weight = 7197.155| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.72 r_work: 0.2764 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3422 Z= 0.195 Angle : 0.595 5.678 4662 Z= 0.304 Chirality : 0.045 0.132 508 Planarity : 0.004 0.046 597 Dihedral : 5.746 55.017 510 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.38 % Allowed : 10.22 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.41), residues: 417 helix: -3.06 (0.87), residues: 27 sheet: 0.52 (0.46), residues: 144 loop : -0.92 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.002 0.001 HIS A 206 PHE 0.011 0.001 PHE A 219 TYR 0.010 0.001 TYR B 369 ARG 0.005 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 1) link_NAG-ASN : angle 0.96181 ( 3) link_BETA1-4 : bond 0.00506 ( 1) link_BETA1-4 : angle 2.48420 ( 3) hydrogen bonds : bond 0.03543 ( 96) hydrogen bonds : angle 5.05191 ( 252) SS BOND : bond 0.00466 ( 6) SS BOND : angle 1.03691 ( 12) covalent geometry : bond 0.00464 ( 3414) covalent geometry : angle 0.58955 ( 4644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8030 (tp30) cc_final: 0.7771 (tp30) REVERT: A 169 GLU cc_start: 0.8459 (tt0) cc_final: 0.7933 (tt0) REVERT: A 214 ASP cc_start: 0.8524 (m-30) cc_final: 0.8196 (m-30) REVERT: B 386 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8227 (pttt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.2149 time to fit residues: 13.7899 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066719 restraints weight = 6933.663| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.64 r_work: 0.2812 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3422 Z= 0.099 Angle : 0.577 6.414 4662 Z= 0.290 Chirality : 0.044 0.138 508 Planarity : 0.004 0.046 597 Dihedral : 5.482 54.668 510 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % Rotamer: Outliers : 1.10 % Allowed : 10.77 % Favored : 88.12 % 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 (0.41), residues: 417 helix: -3.19 (0.79), residues: 27 sheet: 0.56 (0.46), residues: 144 loop : -0.82 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 206 PHE 0.008 0.001 PHE A 203 TYR 0.005 0.001 TYR A 175 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 1) link_NAG-ASN : angle 0.76749 ( 3) link_BETA1-4 : bond 0.00434 ( 1) link_BETA1-4 : angle 2.46329 ( 3) hydrogen bonds : bond 0.02964 ( 96) hydrogen bonds : angle 4.82291 ( 252) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.79152 ( 12) covalent geometry : bond 0.00226 ( 3414) covalent geometry : angle 0.57300 ( 4644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8720 (pm20) cc_final: 0.8400 (pm20) REVERT: A 169 GLU cc_start: 0.8359 (tt0) cc_final: 0.7801 (tt0) REVERT: A 214 ASP cc_start: 0.8545 (m-30) cc_final: 0.8189 (m-30) REVERT: B 386 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8030 (pttt) REVERT: B 444 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8623 (mtmt) outliers start: 4 outliers final: 1 residues processed: 55 average time/residue: 0.2209 time to fit residues: 14.2587 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 6.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063784 restraints weight = 7355.125| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.82 r_work: 0.2760 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3422 Z= 0.196 Angle : 0.631 8.568 4662 Z= 0.314 Chirality : 0.046 0.163 508 Planarity : 0.004 0.046 597 Dihedral : 5.699 54.880 510 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 12.15 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.41), residues: 417 helix: -3.06 (0.88), residues: 27 sheet: 0.50 (0.46), residues: 144 loop : -0.96 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.011 0.001 PHE A 219 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 1) link_NAG-ASN : angle 1.05708 ( 3) link_BETA1-4 : bond 0.00365 ( 1) link_BETA1-4 : angle 2.42141 ( 3) hydrogen bonds : bond 0.03421 ( 96) hydrogen bonds : angle 4.90564 ( 252) SS BOND : bond 0.00439 ( 6) SS BOND : angle 1.07933 ( 12) covalent geometry : bond 0.00470 ( 3414) covalent geometry : angle 0.62575 ( 4644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7572 (pp20) cc_final: 0.7359 (pp20) REVERT: A 104 GLU cc_start: 0.8694 (pm20) cc_final: 0.8285 (pm20) REVERT: A 169 GLU cc_start: 0.8451 (tt0) cc_final: 0.7894 (tt0) REVERT: A 214 ASP cc_start: 0.8489 (m-30) cc_final: 0.8139 (m-30) REVERT: B 386 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8315 (pttt) REVERT: B 444 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8719 (mtmt) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.2276 time to fit residues: 14.5827 Evaluate side-chains 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 189 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.065354 restraints weight = 7161.806| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.81 r_work: 0.2797 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3422 Z= 0.120 Angle : 0.611 8.303 4662 Z= 0.302 Chirality : 0.045 0.161 508 Planarity : 0.004 0.046 597 Dihedral : 5.528 54.952 510 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 0.28 % Allowed : 13.81 % Favored : 85.91 % 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: -0.80 (0.41), residues: 417 helix: -3.24 (0.78), residues: 27 sheet: 0.52 (0.46), residues: 144 loop : -0.86 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.011 0.001 PHE A 83 TYR 0.008 0.001 TYR B 369 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 1) link_NAG-ASN : angle 0.83989 ( 3) link_BETA1-4 : bond 0.00418 ( 1) link_BETA1-4 : angle 2.38783 ( 3) hydrogen bonds : bond 0.03001 ( 96) hydrogen bonds : angle 4.73093 ( 252) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.80516 ( 12) covalent geometry : bond 0.00287 ( 3414) covalent geometry : angle 0.60751 ( 4644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7722 (pp20) cc_final: 0.7515 (pp20) REVERT: A 102 LYS cc_start: 0.8571 (tptp) cc_final: 0.8339 (tptp) REVERT: A 104 GLU cc_start: 0.8438 (pm20) cc_final: 0.8187 (pm20) REVERT: A 169 GLU cc_start: 0.8408 (tt0) cc_final: 0.7825 (tt0) REVERT: A 214 ASP cc_start: 0.8532 (m-30) cc_final: 0.8185 (m-30) REVERT: B 386 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8331 (pttt) REVERT: B 444 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8710 (mtmt) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.2182 time to fit residues: 14.5415 Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0770 chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066533 restraints weight = 6937.513| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.63 r_work: 0.2817 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3422 Z= 0.108 Angle : 0.605 7.921 4662 Z= 0.298 Chirality : 0.044 0.143 508 Planarity : 0.004 0.047 597 Dihedral : 5.435 54.655 510 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.36 % Favored : 96.40 % Rotamer: Outliers : 1.10 % Allowed : 12.98 % Favored : 85.91 % 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: -0.77 (0.41), residues: 417 helix: -3.30 (0.75), residues: 27 sheet: 0.58 (0.46), residues: 144 loop : -0.86 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS A 206 PHE 0.013 0.001 PHE A 83 TYR 0.007 0.001 TYR B 369 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 1) link_NAG-ASN : angle 0.81052 ( 3) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 2.20026 ( 3) hydrogen bonds : bond 0.02964 ( 96) hydrogen bonds : angle 4.66550 ( 252) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.70113 ( 12) covalent geometry : bond 0.00256 ( 3414) covalent geometry : angle 0.60180 ( 4644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8184 (tp30) cc_final: 0.7943 (tp30) REVERT: A 104 GLU cc_start: 0.8481 (pm20) cc_final: 0.8167 (pm20) REVERT: A 169 GLU cc_start: 0.8348 (tt0) cc_final: 0.7725 (tt0) REVERT: A 214 ASP cc_start: 0.8523 (m-30) cc_final: 0.8164 (m-30) REVERT: B 386 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8358 (pttt) REVERT: B 444 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8714 (mtmt) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.2251 time to fit residues: 14.7992 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 189 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065100 restraints weight = 7135.044| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.77 r_work: 0.2795 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3422 Z= 0.144 Angle : 0.640 8.000 4662 Z= 0.319 Chirality : 0.045 0.155 508 Planarity : 0.004 0.046 597 Dihedral : 5.495 54.849 510 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.08 % Favored : 95.68 % Rotamer: Outliers : 0.83 % Allowed : 13.54 % Favored : 85.64 % 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: -0.86 (0.40), residues: 417 helix: -3.28 (0.75), residues: 27 sheet: 0.72 (0.48), residues: 133 loop : -1.01 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.012 0.001 PHE A 83 TYR 0.011 0.001 TYR B 369 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 1) link_NAG-ASN : angle 0.89821 ( 3) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 2.17416 ( 3) hydrogen bonds : bond 0.03085 ( 96) hydrogen bonds : angle 4.63034 ( 252) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.95364 ( 12) covalent geometry : bond 0.00347 ( 3414) covalent geometry : angle 0.63696 ( 4644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8373 (tt0) cc_final: 0.7756 (tt0) REVERT: A 214 ASP cc_start: 0.8510 (m-30) cc_final: 0.8153 (m-30) REVERT: B 444 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8725 (mtmt) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2151 time to fit residues: 13.6099 Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066535 restraints weight = 6955.368| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.65 r_work: 0.2814 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3422 Z= 0.123 Angle : 0.644 7.803 4662 Z= 0.321 Chirality : 0.045 0.158 508 Planarity : 0.004 0.046 597 Dihedral : 5.432 55.005 510 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 14.09 % Favored : 85.08 % 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: -0.80 (0.41), residues: 417 helix: -3.39 (0.71), residues: 27 sheet: 0.55 (0.46), residues: 144 loop : -0.86 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 206 PHE 0.012 0.001 PHE A 83 TYR 0.008 0.001 TYR B 369 ARG 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 1) link_NAG-ASN : angle 0.85630 ( 3) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 2.10167 ( 3) hydrogen bonds : bond 0.02981 ( 96) hydrogen bonds : angle 4.56865 ( 252) SS BOND : bond 0.00339 ( 6) SS BOND : angle 0.82711 ( 12) covalent geometry : bond 0.00296 ( 3414) covalent geometry : angle 0.64157 ( 4644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8361 (tt0) cc_final: 0.7735 (tt0) REVERT: A 214 ASP cc_start: 0.8485 (m-30) cc_final: 0.8118 (m-30) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2232 time to fit residues: 14.1242 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain B residue 395 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.065862 restraints weight = 7033.556| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.66 r_work: 0.2801 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3422 Z= 0.145 Angle : 0.665 7.937 4662 Z= 0.331 Chirality : 0.044 0.147 508 Planarity : 0.004 0.046 597 Dihedral : 5.469 54.970 510 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.08 % Favored : 95.68 % Rotamer: Outliers : 0.83 % Allowed : 14.36 % Favored : 84.81 % 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: -0.84 (0.40), residues: 417 helix: -3.34 (0.73), residues: 27 sheet: 0.53 (0.46), residues: 144 loop : -0.90 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.011 0.001 PHE A 83 TYR 0.011 0.001 TYR B 369 ARG 0.006 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 1) link_NAG-ASN : angle 0.93329 ( 3) link_BETA1-4 : bond 0.00430 ( 1) link_BETA1-4 : angle 2.01922 ( 3) hydrogen bonds : bond 0.03119 ( 96) hydrogen bonds : angle 4.57807 ( 252) SS BOND : bond 0.00373 ( 6) SS BOND : angle 0.87331 ( 12) covalent geometry : bond 0.00352 ( 3414) covalent geometry : angle 0.66195 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2197.64 seconds wall clock time: 38 minutes 50.51 seconds (2330.51 seconds total)