Starting phenix.real_space_refine on Fri Sep 11 03:25:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w4e_65626/09_2026/9w4e_65626.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4460 2.51 5 N 1160 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3481 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3481 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 14, 'TRANS': 413} Chain breaks: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.66, per 1000 atoms: 0.24 Number of scatterers: 6990 At special positions: 0 Unit cell: (83.6, 76, 116.85, 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 46 16.00 O 1324 8.00 N 1160 7.00 C 4460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 393 " - pdb=" SG CYS A 403 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 403 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 495 " 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 NAG-ASN " NAG A 701 " - " ASN A 293 " " NAG B 701 " - " ASN B 293 " Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 359.3 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 34.8% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.842A pdb=" N ILE A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 140 removed outlier: 3.527A pdb=" N ALA A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.805A pdb=" N PHE A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 239 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 298 No H-bonds generated for 'chain 'A' and resid 296 through 298' Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.457A pdb=" N HIS A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.656A pdb=" N LEU B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 78 through 101 removed outlier: 3.857A pdb=" N ILE B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.591A pdb=" N ALA B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 removed outlier: 3.699A pdb=" N PHE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 240 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 309 through 320 removed outlier: 4.375A pdb=" N HIS B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 removed outlier: 4.529A pdb=" N VAL A 484 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 77 removed outlier: 4.199A pdb=" N GLU A 76 " --> pdb=" O LEU A 216 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 213 through 216 current: chain 'A' and resid 333 through 343 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 333 through 343 current: chain 'A' and resid 374 through 378 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 374 through 378 current: chain 'A' and resid 400 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 469 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 50 removed outlier: 4.474A pdb=" N VAL B 484 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 77 removed outlier: 4.220A pdb=" N GLU B 76 " --> pdb=" O LEU B 216 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 213 through 216 current: chain 'B' and resid 333 through 343 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 333 through 343 current: chain 'B' and resid 374 through 378 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 374 through 378 current: chain 'B' and resid 400 through 404 Processing sheet with id=AA7, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AA8, first strand: chain 'B' and resid 477 through 479 249 hydrogen bonds defined for protein. 729 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: 0.77 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2277 1.34 - 1.46: 1273 1.46 - 1.58: 3496 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 7118 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C5 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.413 1.442 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C5 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C3 NAG B 701 " pdb=" O3 NAG B 701 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 7113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 9451 1.75 - 3.49: 170 3.49 - 5.24: 20 5.24 - 6.98: 10 6.98 - 8.73: 1 Bond angle restraints: 9652 Sorted by residual: angle pdb=" N ILE B 221 " pdb=" CA ILE B 221 " pdb=" C ILE B 221 " ideal model delta sigma weight residual 111.91 109.24 2.67 8.90e-01 1.26e+00 9.01e+00 angle pdb=" CB MET A 143 " pdb=" CG MET A 143 " pdb=" SD MET A 143 " ideal model delta sigma weight residual 112.70 121.43 -8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" CA TYR B 459 " pdb=" CB TYR B 459 " pdb=" CG TYR B 459 " ideal model delta sigma weight residual 113.90 119.04 -5.14 1.80e+00 3.09e-01 8.15e+00 angle pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta sigma weight residual 120.55 116.22 4.33 1.58e+00 4.01e-01 7.51e+00 angle pdb=" N ASN B 425 " pdb=" CA ASN B 425 " pdb=" C ASN B 425 " ideal model delta sigma weight residual 113.72 109.73 3.99 1.52e+00 4.33e-01 6.89e+00 ... (remaining 9647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 4025 22.98 - 45.95: 321 45.95 - 68.93: 33 68.93 - 91.91: 4 91.91 - 114.88: 3 Dihedral angle restraints: 4386 sinusoidal: 1828 harmonic: 2558 Sorted by residual: dihedral pdb=" CB CYS B 358 " pdb=" SG CYS B 358 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual -86.00 -152.45 66.45 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -142.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 dihedral pdb=" CB CYS A 108 " pdb=" SG CYS A 108 " pdb=" SG CYS A 241 " pdb=" CB CYS A 241 " ideal model delta sinusoidal sigma weight residual -86.00 -140.89 54.89 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 4383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 770 0.035 - 0.070: 224 0.070 - 0.105: 105 0.105 - 0.139: 24 0.139 - 0.174: 7 Chirality restraints: 1130 Sorted by residual: chirality pdb=" CA MET B 460 " pdb=" N MET B 460 " pdb=" C MET B 460 " pdb=" CB MET B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA VAL A 339 " pdb=" N VAL A 339 " pdb=" C VAL A 339 " pdb=" CB VAL A 339 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1127 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 50 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.91e+00 pdb=" N PRO B 51 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 283 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 284 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 284 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 284 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 283 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 284 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1683 2.80 - 3.32: 6810 3.32 - 3.85: 11593 3.85 - 4.37: 13147 4.37 - 4.90: 22732 Nonbonded interactions: 55965 Sorted by model distance: nonbonded pdb=" OG SER A 378 " pdb=" OD1 ASP A 380 " model vdw 2.274 3.040 nonbonded pdb=" O HIS B 116 " pdb=" OG1 THR B 120 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG A 386 " pdb=" OD2 ASP A 419 " model vdw 2.295 3.120 nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASP B 380 " model vdw 2.302 3.040 nonbonded pdb=" O MET A 291 " pdb=" OG1 THR A 295 " model vdw 2.308 3.040 ... (remaining 55960 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.100 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 7128 Z= 0.144 Angle : 0.596 8.727 9674 Z= 0.318 Chirality : 0.043 0.174 1130 Planarity : 0.005 0.070 1224 Dihedral : 15.435 114.885 2690 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.30), residues: 840 helix: 1.99 (0.31), residues: 314 sheet: -0.54 (0.41), residues: 156 loop : -1.68 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 501 TYR 0.033 0.002 TYR A 459 PHE 0.023 0.001 PHE B 58 TRP 0.022 0.001 TRP B 99 HIS 0.006 0.000 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7118) covalent geometry : angle 0.59391 / 0.32 ( 9652) SS BOND : bond 0.00203 / 0.08 ( 8) SS BOND : angle 0.61973 / 0.32 ( 16) hydrogen bonds : bond 0.11814 / 7.20 ( 249) hydrogen bonds : angle 5.18781 / 3.81 ( 729) link_NAG-ASN : bond 0.00290 / 0.15 ( 2) link_NAG-ASN : angle 2.22553 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.241 Fit side-chains REVERT: A 122 ILE cc_start: 0.8216 (mm) cc_final: 0.7875 (mt) REVERT: A 236 MET cc_start: 0.6809 (mpp) cc_final: 0.6466 (mpp) REVERT: A 248 MET cc_start: 0.7599 (mmt) cc_final: 0.7275 (mmm) REVERT: B 402 LEU cc_start: 0.7836 (mt) cc_final: 0.7451 (mp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0650 time to fit residues: 11.0950 Evaluate side-chains 93 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 252 GLN B 256 ASN B 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.198230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155350 restraints weight = 7552.232| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.94 r_work: 0.3526 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7128 Z= 0.212 Angle : 0.642 9.753 9674 Z= 0.331 Chirality : 0.046 0.201 1130 Planarity : 0.005 0.063 1224 Dihedral : 7.607 88.586 958 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.00 % Allowed : 10.90 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 840 helix: 1.64 (0.30), residues: 326 sheet: -0.78 (0.39), residues: 158 loop : -1.54 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 386 TYR 0.019 0.002 TYR B 459 PHE 0.019 0.002 PHE B 58 TRP 0.018 0.002 TRP B 99 HIS 0.005 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 ( 7118) covalent geometry : angle 0.63908 / 0.33 ( 9652) SS BOND : bond 0.00264 / 0.12 ( 8) SS BOND : angle 1.19471 / 0.56 ( 16) hydrogen bonds : bond 0.03682 / 2.32 ( 249) hydrogen bonds : angle 4.31025 / 3.10 ( 729) link_NAG-ASN : bond 0.00174 / 0.08 ( 2) link_NAG-ASN : angle 1.98931 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.240 Fit side-chains REVERT: A 195 ASP cc_start: 0.7700 (m-30) cc_final: 0.7434 (m-30) REVERT: A 236 MET cc_start: 0.6948 (mpp) cc_final: 0.6646 (mpp) REVERT: A 248 MET cc_start: 0.7878 (mmt) cc_final: 0.7611 (mmm) REVERT: A 282 MET cc_start: 0.8819 (tpp) cc_final: 0.8618 (tpp) REVERT: B 131 GLU cc_start: 0.8494 (tp30) cc_final: 0.8172 (tp30) REVERT: B 219 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7519 (mt-10) REVERT: B 236 MET cc_start: 0.6338 (mpp) cc_final: 0.6106 (mpp) REVERT: B 430 MET cc_start: 0.4216 (ttt) cc_final: 0.3844 (ptm) outliers start: 8 outliers final: 5 residues processed: 116 average time/residue: 0.0688 time to fit residues: 11.1963 Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 0.0670 chunk 52 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.189235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144717 restraints weight = 7493.952| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.97 r_work: 0.3475 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7128 Z= 0.167 Angle : 0.584 11.076 9674 Z= 0.304 Chirality : 0.044 0.165 1130 Planarity : 0.005 0.061 1224 Dihedral : 6.850 75.959 958 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.25 % Allowed : 14.79 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.29), residues: 840 helix: 1.78 (0.30), residues: 326 sheet: -0.76 (0.37), residues: 168 loop : -1.67 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.019 0.002 TYR B 459 PHE 0.018 0.001 PHE B 58 TRP 0.014 0.001 TRP B 99 HIS 0.002 0.000 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 7118) covalent geometry : angle 0.57907 / 0.30 ( 9652) SS BOND : bond 0.00225 / 0.10 ( 8) SS BOND : angle 1.19438 / 0.56 ( 16) hydrogen bonds : bond 0.03383 / 2.13 ( 249) hydrogen bonds : angle 4.15664 / 2.99 ( 729) link_NAG-ASN : bond 0.00102 / 0.05 ( 2) link_NAG-ASN : angle 2.53414 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.259 Fit side-chains REVERT: A 195 ASP cc_start: 0.7632 (m-30) cc_final: 0.7421 (m-30) REVERT: A 347 TYR cc_start: 0.8682 (m-80) cc_final: 0.8466 (m-80) REVERT: B 131 GLU cc_start: 0.8439 (tp30) cc_final: 0.8119 (tp30) REVERT: B 236 MET cc_start: 0.6210 (mpp) cc_final: 0.5959 (mpp) outliers start: 10 outliers final: 8 residues processed: 114 average time/residue: 0.0704 time to fit residues: 11.3116 Evaluate side-chains 106 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.202076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157744 restraints weight = 7638.821| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.76 r_work: 0.3548 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7128 Z= 0.153 Angle : 0.573 10.820 9674 Z= 0.299 Chirality : 0.043 0.151 1130 Planarity : 0.004 0.059 1224 Dihedral : 6.129 55.691 958 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.26 % Allowed : 15.91 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.29), residues: 840 helix: 1.87 (0.31), residues: 326 sheet: -0.87 (0.38), residues: 168 loop : -1.65 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 222 TYR 0.018 0.001 TYR B 459 PHE 0.017 0.001 PHE B 58 TRP 0.012 0.001 TRP B 99 HIS 0.002 0.000 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7118) covalent geometry : angle 0.56367 / 0.30 ( 9652) SS BOND : bond 0.00218 / 0.10 ( 8) SS BOND : angle 1.24707 / 0.58 ( 16) hydrogen bonds : bond 0.03238 / 2.03 ( 249) hydrogen bonds : angle 4.01820 / 2.89 ( 729) link_NAG-ASN : bond 0.00155 / 0.07 ( 2) link_NAG-ASN : angle 3.72854 / 1.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.246 Fit side-chains REVERT: A 128 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7151 (pp20) REVERT: A 195 ASP cc_start: 0.7663 (m-30) cc_final: 0.7434 (m-30) REVERT: B 131 GLU cc_start: 0.8461 (tp30) cc_final: 0.8176 (tp30) REVERT: B 236 MET cc_start: 0.6263 (mpp) cc_final: 0.6003 (mpp) REVERT: B 373 LYS cc_start: 0.7899 (ttmm) cc_final: 0.7681 (ttmt) outliers start: 18 outliers final: 10 residues processed: 121 average time/residue: 0.0719 time to fit residues: 12.1063 Evaluate side-chains 110 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLN Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.202307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.158717 restraints weight = 7627.514| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.53 r_work: 0.3556 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7128 Z= 0.136 Angle : 0.549 6.390 9674 Z= 0.292 Chirality : 0.043 0.148 1130 Planarity : 0.004 0.058 1224 Dihedral : 4.974 22.846 958 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.01 % Allowed : 16.54 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.30), residues: 840 helix: 1.91 (0.31), residues: 326 sheet: -0.94 (0.41), residues: 154 loop : -1.61 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.023 0.001 TYR A 347 PHE 0.016 0.001 PHE B 58 TRP 0.011 0.001 TRP B 99 HIS 0.002 0.000 HIS A 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 7118) covalent geometry : angle 0.54078 / 0.29 ( 9652) SS BOND : bond 0.00203 / 0.08 ( 8) SS BOND : angle 1.49056 / 0.68 ( 16) hydrogen bonds : bond 0.03138 / 1.96 ( 249) hydrogen bonds : angle 3.95908 / 2.84 ( 729) link_NAG-ASN : bond 0.00112 / 0.05 ( 2) link_NAG-ASN : angle 2.96074 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.258 Fit side-chains REVERT: A 128 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7136 (pp20) REVERT: A 195 ASP cc_start: 0.7613 (m-30) cc_final: 0.7399 (m-30) REVERT: B 131 GLU cc_start: 0.8409 (tp30) cc_final: 0.8134 (tp30) REVERT: B 195 ASP cc_start: 0.7627 (m-30) cc_final: 0.7266 (m-30) REVERT: B 236 MET cc_start: 0.6247 (mpp) cc_final: 0.5945 (mpp) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.0698 time to fit residues: 11.6373 Evaluate side-chains 109 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 324 HIS B 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.196933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154653 restraints weight = 7604.535| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.66 r_work: 0.3506 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7128 Z= 0.192 Angle : 0.591 6.359 9674 Z= 0.313 Chirality : 0.044 0.143 1130 Planarity : 0.004 0.060 1224 Dihedral : 5.040 24.022 958 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.88 % Allowed : 17.67 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.29), residues: 840 helix: 1.76 (0.30), residues: 326 sheet: -1.04 (0.41), residues: 154 loop : -1.65 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.028 0.002 TYR A 347 PHE 0.020 0.001 PHE B 58 TRP 0.012 0.002 TRP B 99 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 7118) covalent geometry : angle 0.58501 / 0.31 ( 9652) SS BOND : bond 0.00298 / 0.12 ( 8) SS BOND : angle 1.34433 / 0.61 ( 16) hydrogen bonds : bond 0.03429 / 2.15 ( 249) hydrogen bonds : angle 4.07405 / 2.93 ( 729) link_NAG-ASN : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : angle 2.63397 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.249 Fit side-chains REVERT: A 95 ASN cc_start: 0.8082 (m110) cc_final: 0.7840 (m110) REVERT: A 195 ASP cc_start: 0.7699 (m-30) cc_final: 0.7478 (m-30) REVERT: B 131 GLU cc_start: 0.8416 (tp30) cc_final: 0.8158 (tp30) REVERT: B 236 MET cc_start: 0.6378 (mpp) cc_final: 0.6078 (mpp) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.0665 time to fit residues: 11.9376 Evaluate side-chains 115 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 400 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 ASN B 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.158126 restraints weight = 7677.674| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.72 r_work: 0.3551 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7128 Z= 0.151 Angle : 0.572 6.662 9674 Z= 0.303 Chirality : 0.043 0.149 1130 Planarity : 0.004 0.058 1224 Dihedral : 4.975 23.394 958 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.88 % Allowed : 18.67 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.29), residues: 840 helix: 1.80 (0.30), residues: 326 sheet: -1.00 (0.41), residues: 154 loop : -1.69 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 386 TYR 0.024 0.002 TYR A 347 PHE 0.018 0.001 PHE B 58 TRP 0.017 0.001 TRP B 99 HIS 0.002 0.000 HIS B 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 7118) covalent geometry : angle 0.56498 / 0.30 ( 9652) SS BOND : bond 0.00211 / 0.09 ( 8) SS BOND : angle 1.77369 / 0.80 ( 16) hydrogen bonds : bond 0.03254 / 2.03 ( 249) hydrogen bonds : angle 4.00189 / 2.88 ( 729) link_NAG-ASN : bond 0.00051 / 0.02 ( 2) link_NAG-ASN : angle 2.25109 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.173 Fit side-chains REVERT: A 58 PHE cc_start: 0.8293 (m-80) cc_final: 0.7842 (m-80) REVERT: A 95 ASN cc_start: 0.8070 (m110) cc_final: 0.7808 (m110) REVERT: A 195 ASP cc_start: 0.7654 (m-30) cc_final: 0.7434 (m-30) REVERT: B 131 GLU cc_start: 0.8386 (tp30) cc_final: 0.8122 (tp30) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 0.0689 time to fit residues: 11.2791 Evaluate side-chains 112 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.201683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.159083 restraints weight = 7689.404| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.77 r_work: 0.3550 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7128 Z= 0.145 Angle : 0.583 6.023 9674 Z= 0.310 Chirality : 0.043 0.147 1130 Planarity : 0.004 0.058 1224 Dihedral : 4.889 22.902 958 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.88 % Allowed : 19.42 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 840 helix: 1.83 (0.31), residues: 326 sheet: -1.01 (0.42), residues: 154 loop : -1.72 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.020 0.002 TYR A 347 PHE 0.018 0.001 PHE B 58 TRP 0.018 0.001 TRP B 99 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7118) covalent geometry : angle 0.57748 / 0.31 ( 9652) SS BOND : bond 0.00239 / 0.09 ( 8) SS BOND : angle 1.61185 / 0.72 ( 16) hydrogen bonds : bond 0.03243 / 2.02 ( 249) hydrogen bonds : angle 3.99837 / 2.87 ( 729) link_NAG-ASN : bond 0.00018 / 0.01 ( 2) link_NAG-ASN : angle 2.17251 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.240 Fit side-chains REVERT: A 95 ASN cc_start: 0.8069 (m110) cc_final: 0.7803 (m110) REVERT: A 128 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7214 (pp20) REVERT: A 195 ASP cc_start: 0.7621 (m-30) cc_final: 0.7405 (m-30) REVERT: B 131 GLU cc_start: 0.8384 (tp30) cc_final: 0.8125 (tp30) REVERT: B 236 MET cc_start: 0.6674 (mpp) cc_final: 0.6434 (mpp) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 0.0628 time to fit residues: 10.4471 Evaluate side-chains 115 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 425 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 78 optimal weight: 0.0060 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.203786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.162561 restraints weight = 7658.029| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.49 r_work: 0.3583 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7128 Z= 0.120 Angle : 0.568 6.257 9674 Z= 0.303 Chirality : 0.043 0.158 1130 Planarity : 0.004 0.057 1224 Dihedral : 4.781 21.817 958 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.75 % Allowed : 20.18 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 840 helix: 1.87 (0.31), residues: 324 sheet: -1.03 (0.42), residues: 154 loop : -1.73 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.018 0.001 TYR B 459 PHE 0.020 0.001 PHE B 58 TRP 0.017 0.001 TRP B 99 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7118) covalent geometry : angle 0.56391 / 0.30 ( 9652) SS BOND : bond 0.00203 / 0.08 ( 8) SS BOND : angle 1.36870 / 0.61 ( 16) hydrogen bonds : bond 0.03165 / 1.97 ( 249) hydrogen bonds : angle 3.94055 / 2.82 ( 729) link_NAG-ASN : bond 0.00036 / 0.02 ( 2) link_NAG-ASN : angle 1.93940 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.253 Fit side-chains REVERT: A 58 PHE cc_start: 0.8225 (m-80) cc_final: 0.7790 (m-80) REVERT: A 128 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7195 (pp20) REVERT: A 195 ASP cc_start: 0.7535 (m-30) cc_final: 0.7323 (m-30) REVERT: B 131 GLU cc_start: 0.8345 (tp30) cc_final: 0.8085 (tp30) REVERT: B 236 MET cc_start: 0.6567 (mpp) cc_final: 0.6296 (mpp) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.0699 time to fit residues: 11.0163 Evaluate side-chains 108 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.201732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159029 restraints weight = 7673.424| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.78 r_work: 0.3552 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7128 Z= 0.156 Angle : 0.591 6.969 9674 Z= 0.311 Chirality : 0.044 0.157 1130 Planarity : 0.004 0.058 1224 Dihedral : 4.826 22.777 958 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.50 % Allowed : 20.93 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.30), residues: 840 helix: 1.79 (0.30), residues: 326 sheet: -1.16 (0.41), residues: 156 loop : -1.64 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.019 0.002 TYR A 347 PHE 0.018 0.001 PHE B 58 TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7118) covalent geometry : angle 0.58636 / 0.31 ( 9652) SS BOND : bond 0.00249 / 0.09 ( 8) SS BOND : angle 1.52570 / 0.70 ( 16) hydrogen bonds : bond 0.03311 / 2.07 ( 249) hydrogen bonds : angle 4.01042 / 2.87 ( 729) link_NAG-ASN : bond 0.00051 / 0.02 ( 2) link_NAG-ASN : angle 2.02825 / 1.01 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.257 Fit side-chains REVERT: A 128 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7209 (pp20) REVERT: B 131 GLU cc_start: 0.8401 (tp30) cc_final: 0.8146 (tp30) REVERT: B 236 MET cc_start: 0.6621 (mpp) cc_final: 0.6372 (mpp) REVERT: B 425 ASN cc_start: 0.6039 (OUTLIER) cc_final: 0.5819 (t0) outliers start: 12 outliers final: 10 residues processed: 114 average time/residue: 0.0613 time to fit residues: 9.9425 Evaluate side-chains 116 residues out of total 798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 425 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.199238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158500 restraints weight = 7557.661| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.57 r_work: 0.3565 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7128 Z= 0.155 Angle : 0.588 6.974 9674 Z= 0.311 Chirality : 0.044 0.155 1130 Planarity : 0.004 0.058 1224 Dihedral : 4.838 22.925 958 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.75 % Allowed : 21.68 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 840 helix: 1.70 (0.30), residues: 326 sheet: -1.14 (0.41), residues: 154 loop : -1.68 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 386 TYR 0.019 0.002 TYR A 347 PHE 0.020 0.001 PHE B 58 TRP 0.017 0.001 TRP B 99 HIS 0.002 0.000 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 7118) covalent geometry : angle 0.58368 / 0.31 ( 9652) SS BOND : bond 0.00222 / 0.09 ( 8) SS BOND : angle 1.46528 / 0.67 ( 16) hydrogen bonds : bond 0.03304 / 2.06 ( 249) hydrogen bonds : angle 4.03531 / 2.90 ( 729) link_NAG-ASN : bond 0.00078 / 0.04 ( 2) link_NAG-ASN : angle 1.91360 / 0.97 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1524.23 seconds wall clock time: 26 minutes 55.57 seconds (1615.57 seconds total)