Starting phenix.real_space_refine on Sat May 10 11:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ykh_39372/05_2025/8ykh_39372.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ykh_39372/05_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_39372/05_2025/8ykh_39372.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ykh_39372/05_2025/8ykh_39372.map" model { file = "/net/cci-nas-00/data/ceres_data/8ykh_39372/05_2025/8ykh_39372.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ykh_39372/05_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-5687/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: 3.53, per 1000 atoms: 1.06 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: 0.85 Conformation dependent library (CDL) restraints added in 440.7 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: 0.53 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: 0.99 Time building geometry restraints manager: 0.99 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- 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 : 0.409 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: 0.2545 time to fit residues: 16.4098 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 : 0.406 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.093663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.065376 restraints weight = 7075.016| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.86 r_work: 0.2760 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3422 Z= 0.104 Angle : 0.596 6.188 4662 Z= 0.303 Chirality : 0.046 0.143 508 Planarity : 0.004 0.048 597 Dihedral : 5.684 54.264 510 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -2.69 (0.95), residues: 21 sheet: 0.72 (0.47), residues: 137 loop : -0.88 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.000 0.000 HIS A 206 PHE 0.009 0.001 PHE A 203 TYR 0.006 0.001 TYR A 49 ARG 0.003 0.000 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 1) link_NAG-ASN : angle 0.88322 ( 3) link_BETA1-4 : bond 0.00453 ( 1) link_BETA1-4 : angle 2.57513 ( 3) hydrogen bonds : bond 0.03532 ( 96) hydrogen bonds : angle 5.27869 ( 252) SS BOND : bond 0.00436 ( 6) SS BOND : angle 0.84111 ( 12) covalent geometry : bond 0.00235 ( 3414) covalent geometry : angle 0.59172 ( 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 : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7932 (tp30) cc_final: 0.7621 (tp30) REVERT: A 169 GLU cc_start: 0.8467 (tt0) cc_final: 0.7838 (tt0) REVERT: A 214 ASP cc_start: 0.8618 (m-30) cc_final: 0.8194 (m-30) REVERT: B 386 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8029 (ttpt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2432 time to fit residues: 16.7842 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 : 0.389 ------------------------------------------------------------------------------- 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: 0.4980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.094320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.065890 restraints weight = 7048.128| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.76 r_work: 0.2805 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1335 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= 0.100 Angle : 0.560 5.915 4662 Z= 0.284 Chirality : 0.045 0.143 508 Planarity : 0.004 0.049 597 Dihedral : 5.532 54.488 510 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: -0.70 (0.41), residues: 417 helix: -3.14 (0.78), residues: 27 sheet: 0.82 (0.49), residues: 131 loop : -0.87 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 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 0.00374 ( 1) link_NAG-ASN : angle 0.81362 ( 3) link_BETA1-4 : bond 0.00451 ( 1) link_BETA1-4 : angle 2.44176 ( 3) hydrogen bonds : bond 0.03178 ( 96) hydrogen bonds : angle 4.99739 ( 252) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.71385 ( 12) covalent geometry : bond 0.00228 ( 3414) covalent geometry : angle 0.55617 ( 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 : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7873 (tp30) cc_final: 0.7620 (tp30) REVERT: A 169 GLU cc_start: 0.8424 (tt0) cc_final: 0.7938 (tt0) REVERT: A 214 ASP cc_start: 0.8505 (m-30) cc_final: 0.8173 (m-30) REVERT: B 386 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8146 (ttpt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2288 time to fit residues: 14.7226 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 : 0.409 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.091457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.063550 restraints weight = 7225.779| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.70 r_work: 0.2741 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3422 Z= 0.248 Angle : 0.636 5.802 4662 Z= 0.324 Chirality : 0.046 0.134 508 Planarity : 0.004 0.047 597 Dihedral : 5.900 55.195 510 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % 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: -0.92 (0.40), residues: 417 helix: -2.93 (0.94), residues: 27 sheet: 0.68 (0.48), residues: 133 loop : -1.09 (0.36), residues: 257 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 0.013 0.002 PHE A 219 TYR 0.012 0.002 TYR B 473 ARG 0.005 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00391 ( 1) link_NAG-ASN : angle 1.24850 ( 3) link_BETA1-4 : bond 0.00535 ( 1) link_BETA1-4 : angle 2.51007 ( 3) hydrogen bonds : bond 0.03782 ( 96) hydrogen bonds : angle 5.13336 ( 252) SS BOND : bond 0.00528 ( 6) SS BOND : angle 1.20207 ( 12) covalent geometry : bond 0.00595 ( 3414) covalent geometry : angle 0.63011 ( 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 : 0.362 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8120 (tp30) cc_final: 0.7867 (tp30) REVERT: A 81 GLU cc_start: 0.7656 (pp20) cc_final: 0.7399 (pp20) REVERT: A 169 GLU cc_start: 0.8456 (tt0) cc_final: 0.7898 (tt0) REVERT: A 214 ASP cc_start: 0.8480 (m-30) cc_final: 0.8149 (m-30) REVERT: B 386 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8268 (pttt) REVERT: B 444 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8774 (mtmt) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.2197 time to fit residues: 14.1028 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 : 0.359 ------------------------------------------------------------------------------- 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: 0.0370 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.0870 chunk 30 optimal weight: 0.2980 chunk 23 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.095192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.067729 restraints weight = 6924.429| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.65 r_work: 0.2840 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3422 Z= 0.093 Angle : 0.580 7.253 4662 Z= 0.292 Chirality : 0.044 0.142 508 Planarity : 0.004 0.047 597 Dihedral : 5.419 54.599 510 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 11.05 % 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: -0.65 (0.41), residues: 417 helix: -2.59 (0.98), residues: 21 sheet: 0.76 (0.48), residues: 133 loop : -0.91 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.000 0.000 HIS A 206 PHE 0.009 0.001 PHE A 83 TYR 0.005 0.001 TYR B 380 ARG 0.003 0.000 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 1) link_NAG-ASN : angle 0.91121 ( 3) link_BETA1-4 : bond 0.00337 ( 1) link_BETA1-4 : angle 2.46550 ( 3) hydrogen bonds : bond 0.02823 ( 96) hydrogen bonds : angle 4.75648 ( 252) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.64258 ( 12) covalent geometry : bond 0.00200 ( 3414) covalent geometry : angle 0.57650 ( 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 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7780 (pp20) cc_final: 0.7542 (pp20) REVERT: A 169 GLU cc_start: 0.8318 (tt0) cc_final: 0.7749 (tt0) REVERT: A 214 ASP cc_start: 0.8552 (m-30) cc_final: 0.8198 (m-30) REVERT: B 386 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8007 (pttt) REVERT: B 444 LYS cc_start: 0.8967 (mtpp) cc_final: 0.8679 (mtmt) outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.2244 time to fit residues: 14.1072 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 : 0.368 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.092272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063682 restraints weight = 7350.682| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.84 r_work: 0.2759 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1734 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= 0.200 Angle : 0.629 8.081 4662 Z= 0.315 Chirality : 0.046 0.156 508 Planarity : 0.004 0.046 597 Dihedral : 5.696 54.726 510 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 1.10 % Allowed : 11.88 % 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: -0.86 (0.41), residues: 417 helix: -3.11 (0.85), residues: 27 sheet: 0.74 (0.48), residues: 133 loop : -1.04 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.012 0.002 PHE A 83 TYR 0.017 0.001 TYR B 369 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 1) link_NAG-ASN : angle 1.09877 ( 3) link_BETA1-4 : bond 0.00526 ( 1) link_BETA1-4 : angle 2.34492 ( 3) hydrogen bonds : bond 0.03466 ( 96) hydrogen bonds : angle 4.87778 ( 252) SS BOND : bond 0.00454 ( 6) SS BOND : angle 1.11059 ( 12) covalent geometry : bond 0.00478 ( 3414) covalent geometry : angle 0.62426 ( 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: 4 poor density : 54 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8333 (tp30) cc_final: 0.8128 (tp30) REVERT: A 81 GLU cc_start: 0.7989 (pp20) cc_final: 0.7722 (pp20) REVERT: A 169 GLU cc_start: 0.8441 (tt0) cc_final: 0.7888 (tt0) REVERT: A 214 ASP cc_start: 0.8496 (m-30) cc_final: 0.8155 (m-30) REVERT: B 386 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8320 (pttt) REVERT: B 444 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8707 (mtmt) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 0.2251 time to fit residues: 14.4410 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 : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE 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: 0.9980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.092586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.064086 restraints weight = 7193.919| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.78 r_work: 0.2771 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3422 Z= 0.170 Angle : 0.628 8.330 4662 Z= 0.312 Chirality : 0.045 0.170 508 Planarity : 0.004 0.046 597 Dihedral : 5.662 55.198 510 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.60 % Favored : 96.16 % Rotamer: Outliers : 1.10 % Allowed : 12.43 % Favored : 86.46 % 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: -0.91 (0.40), residues: 417 helix: -3.19 (0.82), residues: 27 sheet: 0.69 (0.48), residues: 133 loop : -1.05 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.011 0.001 PHE A 83 TYR 0.012 0.001 TYR B 369 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00429 ( 1) link_NAG-ASN : angle 1.02361 ( 3) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 2.40880 ( 3) hydrogen bonds : bond 0.03229 ( 96) hydrogen bonds : angle 4.78978 ( 252) SS BOND : bond 0.00405 ( 6) SS BOND : angle 0.95306 ( 12) covalent geometry : bond 0.00408 ( 3414) covalent geometry : angle 0.62422 ( 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 61 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8113 (pp20) cc_final: 0.7849 (pp20) REVERT: A 102 LYS cc_start: 0.8541 (tptp) cc_final: 0.8231 (tptp) REVERT: A 104 GLU cc_start: 0.8516 (pm20) cc_final: 0.8195 (pm20) REVERT: A 169 GLU cc_start: 0.8436 (tt0) cc_final: 0.7875 (tt0) REVERT: A 214 ASP cc_start: 0.8473 (m-30) cc_final: 0.8115 (m-30) REVERT: B 386 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8345 (pttt) outliers start: 4 outliers final: 2 residues processed: 59 average time/residue: 0.2203 time to fit residues: 15.1211 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE 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: 2.9990 chunk 5 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 0.0470 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.093224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.064792 restraints weight = 7115.469| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.78 r_work: 0.2780 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3422 Z= 0.147 Angle : 0.636 8.153 4662 Z= 0.311 Chirality : 0.045 0.151 508 Planarity : 0.004 0.045 597 Dihedral : 5.594 55.010 510 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.60 % Favored : 96.16 % Rotamer: Outliers : 1.10 % Allowed : 12.71 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.40), residues: 417 helix: -3.35 (0.77), residues: 27 sheet: 0.69 (0.48), residues: 133 loop : -1.07 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.003 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 1) link_NAG-ASN : angle 0.95371 ( 3) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 2.28284 ( 3) hydrogen bonds : bond 0.03135 ( 96) hydrogen bonds : angle 4.72929 ( 252) SS BOND : bond 0.00371 ( 6) SS BOND : angle 0.86778 ( 12) covalent geometry : bond 0.00352 ( 3414) covalent geometry : angle 0.63223 ( 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 : 0.354 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8212 (pp20) cc_final: 0.7929 (pp20) REVERT: A 102 LYS cc_start: 0.8517 (tptp) cc_final: 0.8229 (tptp) REVERT: A 104 GLU cc_start: 0.8568 (pm20) cc_final: 0.8166 (pm20) REVERT: A 169 GLU cc_start: 0.8406 (tt0) cc_final: 0.7825 (tt0) REVERT: A 214 ASP cc_start: 0.8473 (m-30) cc_final: 0.8114 (m-30) REVERT: B 386 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8373 (pttt) REVERT: B 444 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8683 (mtmt) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 0.2163 time to fit residues: 13.8938 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 : 0.400 ------------------------------------------------------------------------------- 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: 2.9990 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.0000 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 overall best weight: 0.3562 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.094689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.066430 restraints weight = 6990.715| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.75 r_work: 0.2813 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3422 Z= 0.097 Angle : 0.624 7.632 4662 Z= 0.306 Chirality : 0.044 0.147 508 Planarity : 0.004 0.046 597 Dihedral : 5.360 54.713 510 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.84 % Favored : 95.92 % Rotamer: Outliers : 0.28 % Allowed : 14.64 % 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: -0.83 (0.41), residues: 417 helix: -3.46 (0.70), residues: 27 sheet: 0.75 (0.48), residues: 133 loop : -0.96 (0.37), residues: 257 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 83 TYR 0.005 0.001 TYR B 369 ARG 0.002 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 1) link_NAG-ASN : angle 0.84713 ( 3) link_BETA1-4 : bond 0.00396 ( 1) link_BETA1-4 : angle 2.14377 ( 3) hydrogen bonds : bond 0.02781 ( 96) hydrogen bonds : angle 4.58710 ( 252) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.86881 ( 12) covalent geometry : bond 0.00225 ( 3414) covalent geometry : angle 0.62052 ( 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 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8260 (pp20) cc_final: 0.7970 (pp20) REVERT: A 104 GLU cc_start: 0.8599 (pm20) cc_final: 0.8146 (pm20) REVERT: A 169 GLU cc_start: 0.8345 (tt0) cc_final: 0.7709 (tt0) REVERT: A 214 ASP cc_start: 0.8521 (m-30) cc_final: 0.8175 (m-30) REVERT: B 444 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8637 (mtmt) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2272 time to fit residues: 14.1699 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS 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: 0.0870 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.094182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.066005 restraints weight = 6974.206| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.73 r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2041 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= 0.119 Angle : 0.640 7.417 4662 Z= 0.317 Chirality : 0.044 0.149 508 Planarity : 0.004 0.046 597 Dihedral : 5.386 55.033 510 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.60 % Favored : 96.16 % Rotamer: Outliers : 0.55 % Allowed : 14.36 % 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: -3.33 (0.73), residues: 27 sheet: 0.79 (0.48), residues: 133 loop : -0.96 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 206 PHE 0.009 0.001 PHE A 83 TYR 0.008 0.001 TYR B 369 ARG 0.005 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 1) link_NAG-ASN : angle 0.84395 ( 3) link_BETA1-4 : bond 0.00436 ( 1) link_BETA1-4 : angle 2.03133 ( 3) hydrogen bonds : bond 0.02909 ( 96) hydrogen bonds : angle 4.53745 ( 252) SS BOND : bond 0.00334 ( 6) SS BOND : angle 0.84603 ( 12) covalent geometry : bond 0.00286 ( 3414) covalent geometry : angle 0.63782 ( 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 55 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8296 (pp20) cc_final: 0.8009 (pp20) REVERT: A 169 GLU cc_start: 0.8352 (tt0) cc_final: 0.7701 (tt0) REVERT: A 214 ASP cc_start: 0.8494 (m-30) cc_final: 0.8136 (m-30) REVERT: B 444 LYS cc_start: 0.9004 (mtpp) cc_final: 0.8630 (mtmt) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2267 time to fit residues: 14.0443 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 189 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.095075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066889 restraints weight = 6989.149| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.74 r_work: 0.2819 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3422 Z= 0.108 Angle : 0.641 7.825 4662 Z= 0.317 Chirality : 0.044 0.149 508 Planarity : 0.004 0.047 597 Dihedral : 5.314 54.886 510 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.36 % Favored : 96.40 % Rotamer: Outliers : 0.55 % Allowed : 14.64 % 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: -0.79 (0.41), residues: 417 helix: -3.42 (0.70), residues: 27 sheet: 0.78 (0.49), residues: 131 loop : -0.92 (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 0.008 0.001 PHE A 83 TYR 0.006 0.001 TYR B 369 ARG 0.006 0.000 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 1) link_NAG-ASN : angle 0.87109 ( 3) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 1.98634 ( 3) hydrogen bonds : bond 0.02836 ( 96) hydrogen bonds : angle 4.51448 ( 252) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.74201 ( 12) covalent geometry : bond 0.00259 ( 3414) covalent geometry : angle 0.63856 ( 4644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.82 seconds wall clock time: 39 minutes 9.84 seconds (2349.84 seconds total)