Starting phenix.real_space_refine on Fri Aug 22 18:02:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g3g_50998/08_2025/9g3g_50998.map" } resolution = 3.07 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= -0.000 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 20 5.16 5 C 4358 2.51 5 N 1026 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6482 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3200 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 14, 'TRANS': 378} Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3184 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.89, per 1000 atoms: 0.29 Number of scatterers: 6482 At special positions: 0 Unit cell: (93.002, 65.408, 100.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 2 15.00 O 1076 8.00 N 1026 7.00 C 4358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 303.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 90.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.516A pdb=" N PHE A 13 " --> pdb=" O PRO A 9 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.651A pdb=" N ARG A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 54 through 79 Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 88 through 125 removed outlier: 4.288A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 130 through 177 removed outlier: 3.880A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 227 removed outlier: 3.538A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 262 removed outlier: 3.525A pdb=" N ILE A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 287 removed outlier: 4.456A pdb=" N GLY A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 337 removed outlier: 3.926A pdb=" N GLU A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.669A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 394 removed outlier: 3.557A pdb=" N LEU A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.573A pdb=" N PHE B 13 " --> pdb=" O PRO B 9 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 48 through 53 removed outlier: 3.659A pdb=" N ARG B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 53' Processing helix chain 'B' and resid 54 through 79 removed outlier: 3.522A pdb=" N SER B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 125 removed outlier: 4.270A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 130 through 177 removed outlier: 3.915A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 186 through 227 removed outlier: 4.366A pdb=" N THR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 262 Processing helix chain 'B' and resid 263 through 289 removed outlier: 4.428A pdb=" N GLY B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 337 removed outlier: 3.896A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.769A pdb=" N LEU B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 392 removed outlier: 3.894A pdb=" N GLU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA2, first strand: chain 'B' and resid 232 through 233 537 hydrogen bonds defined for protein. 1605 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: 0.91 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1000 1.32 - 1.44: 2038 1.44 - 1.56: 3606 1.56 - 1.68: 4 1.68 - 1.80: 38 Bond restraints: 6686 Sorted by residual: bond pdb=" CA ILE A 239 " pdb=" CB ILE A 239 " ideal model delta sigma weight residual 1.537 1.550 -0.013 1.29e-02 6.01e+03 1.02e+00 bond pdb=" CA ILE A 239 " pdb=" C ILE A 239 " ideal model delta sigma weight residual 1.524 1.515 0.009 1.05e-02 9.07e+03 7.66e-01 bond pdb=" C ALA A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.335 1.343 -0.009 1.28e-02 6.10e+03 4.57e-01 bond pdb=" CB GLN A 179 " pdb=" CG GLN A 179 " ideal model delta sigma weight residual 1.520 1.540 -0.020 3.00e-02 1.11e+03 4.39e-01 bond pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 1.465 1.478 -0.013 2.03e-02 2.43e+03 4.21e-01 ... (remaining 6681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8989 1.39 - 2.78: 86 2.78 - 4.17: 13 4.17 - 5.56: 8 5.56 - 6.95: 4 Bond angle restraints: 9100 Sorted by residual: angle pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " pdb=" CG LEU B 376 " ideal model delta sigma weight residual 116.30 123.25 -6.95 3.50e+00 8.16e-02 3.95e+00 angle pdb=" N ILE B 235 " pdb=" CA ILE B 235 " pdb=" C ILE B 235 " ideal model delta sigma weight residual 109.34 113.46 -4.12 2.08e+00 2.31e-01 3.92e+00 angle pdb=" CA PRO A 295 " pdb=" C PRO A 295 " pdb=" N PRO A 296 " ideal model delta sigma weight residual 117.93 120.27 -2.34 1.20e+00 6.94e-01 3.80e+00 angle pdb=" N PRO A 295 " pdb=" CA PRO A 295 " pdb=" C PRO A 295 " ideal model delta sigma weight residual 110.70 113.05 -2.35 1.22e+00 6.72e-01 3.71e+00 angle pdb=" C HIS B 391 " pdb=" N GLU B 392 " pdb=" CA GLU B 392 " ideal model delta sigma weight residual 121.70 125.16 -3.46 1.80e+00 3.09e-01 3.70e+00 ... (remaining 9095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 3706 34.32 - 68.63: 92 68.63 - 102.95: 2 102.95 - 137.27: 0 137.27 - 171.58: 2 Dihedral angle restraints: 3802 sinusoidal: 1510 harmonic: 2292 Sorted by residual: dihedral pdb=" C3 PGT A 501 " pdb=" C1 PGT A 501 " pdb=" C2 PGT A 501 " pdb=" O3P PGT A 501 " ideal model delta sinusoidal sigma weight residual -66.13 105.45 -171.58 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C3 PGT B 501 " pdb=" C1 PGT B 501 " pdb=" C2 PGT B 501 " pdb=" O3P PGT B 501 " ideal model delta sinusoidal sigma weight residual -66.13 105.39 -171.52 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA ALA B 293 " pdb=" C ALA B 293 " pdb=" N THR B 294 " pdb=" CA THR B 294 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 3799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 670 0.027 - 0.055: 197 0.055 - 0.082: 98 0.082 - 0.110: 28 0.110 - 0.137: 10 Chirality restraints: 1003 Sorted by residual: chirality pdb=" CG LEU B 376 " pdb=" CB LEU B 376 " pdb=" CD1 LEU B 376 " pdb=" CD2 LEU B 376 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE A 239 " pdb=" N ILE A 239 " pdb=" C ILE A 239 " pdb=" CB ILE A 239 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1000 not shown) Planarity restraints: 1107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 125 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 126 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 295 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 296 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 296 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 296 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 294 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 295 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.020 5.00e-02 4.00e+02 ... (remaining 1104 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1272 2.77 - 3.30: 6393 3.30 - 3.84: 10706 3.84 - 4.37: 12864 4.37 - 4.90: 22730 Nonbonded interactions: 53965 Sorted by model distance: nonbonded pdb=" OH TYR B 174 " pdb=" OE2 GLU B 390 " model vdw 2.238 3.040 nonbonded pdb=" NZ LYS A 281 " pdb=" OH TYR A 285 " model vdw 2.283 3.120 nonbonded pdb=" OD1 ASP B 289 " pdb=" OG1 THR B 291 " model vdw 2.287 3.040 nonbonded pdb=" NZ LYS B 281 " pdb=" OH TYR B 285 " model vdw 2.316 3.120 nonbonded pdb=" O SER B 87 " pdb=" OG1 THR B 91 " model vdw 2.350 3.040 ... (remaining 53960 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 392 or resid 501)) 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: 1.120 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.680 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6686 Z= 0.091 Angle : 0.406 6.952 9100 Z= 0.218 Chirality : 0.036 0.137 1003 Planarity : 0.004 0.076 1107 Dihedral : 15.444 171.583 2334 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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 aren not related in a simple way. whole: 1.59 (0.28), residues: 780 helix: 1.49 (0.19), residues: 651 sheet: None (None), residues: 0 loop : -1.07 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.007 0.001 TYR A 316 PHE 0.013 0.001 PHE A 389 TRP 0.011 0.001 TRP A 34 HIS 0.001 0.000 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6686) covalent geometry : angle 0.40637 ( 9100) hydrogen bonds : bond 0.20840 ( 537) hydrogen bonds : angle 7.09534 ( 1605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.246 Fit side-chains REVERT: B 253 MET cc_start: 0.6898 (ttp) cc_final: 0.5934 (mtt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0886 time to fit residues: 11.7245 Evaluate side-chains 85 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN B 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.131311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104298 restraints weight = 6959.545| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.29 r_work: 0.2970 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6686 Z= 0.206 Angle : 0.513 6.644 9100 Z= 0.276 Chirality : 0.042 0.135 1003 Planarity : 0.005 0.055 1107 Dihedral : 11.995 176.243 954 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.76 % Allowed : 4.83 % Favored : 94.41 % 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 aren not related in a simple way. whole: 2.41 (0.28), residues: 780 helix: 2.09 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -1.12 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.008 0.001 TYR A 116 PHE 0.019 0.002 PHE A 389 TRP 0.022 0.001 TRP A 34 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6686) covalent geometry : angle 0.51333 ( 9100) hydrogen bonds : bond 0.05967 ( 537) hydrogen bonds : angle 4.56925 ( 1605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.295 Fit side-chains REVERT: A 376 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7919 (tp) outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.0852 time to fit residues: 10.3182 Evaluate side-chains 87 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.133432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.106290 restraints weight = 6901.620| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.32 r_work: 0.2919 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6686 Z= 0.136 Angle : 0.457 6.865 9100 Z= 0.242 Chirality : 0.039 0.131 1003 Planarity : 0.004 0.045 1107 Dihedral : 10.952 176.513 954 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.91 % Allowed : 6.34 % Favored : 92.75 % 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 aren not related in a simple way. whole: 2.70 (0.28), residues: 780 helix: 2.27 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -0.99 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.008 0.001 TYR B 116 PHE 0.014 0.001 PHE A 389 TRP 0.017 0.001 TRP A 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6686) covalent geometry : angle 0.45706 ( 9100) hydrogen bonds : bond 0.04977 ( 537) hydrogen bonds : angle 4.14192 ( 1605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.252 Fit side-chains REVERT: A 376 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7921 (tp) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.0892 time to fit residues: 11.5026 Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.134051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.106757 restraints weight = 6928.211| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.32 r_work: 0.2943 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6686 Z= 0.133 Angle : 0.454 7.327 9100 Z= 0.238 Chirality : 0.039 0.172 1003 Planarity : 0.004 0.045 1107 Dihedral : 10.244 169.736 954 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.76 % Allowed : 8.01 % Favored : 91.24 % 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 aren not related in a simple way. whole: 2.82 (0.28), residues: 780 helix: 2.35 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.008 0.001 TYR A 116 PHE 0.013 0.001 PHE A 164 TRP 0.014 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6686) covalent geometry : angle 0.45435 ( 9100) hydrogen bonds : bond 0.04741 ( 537) hydrogen bonds : angle 4.02627 ( 1605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.240 Fit side-chains REVERT: A 376 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7810 (tp) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.0841 time to fit residues: 9.9855 Evaluate side-chains 86 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.133255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.106105 restraints weight = 6985.882| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.32 r_work: 0.2901 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6686 Z= 0.144 Angle : 0.461 6.756 9100 Z= 0.242 Chirality : 0.039 0.169 1003 Planarity : 0.004 0.045 1107 Dihedral : 9.847 161.279 954 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.06 % Allowed : 8.61 % Favored : 90.33 % 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 aren not related in a simple way. whole: 2.82 (0.28), residues: 780 helix: 2.35 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.023 0.001 PHE B 26 TRP 0.019 0.001 TRP B 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6686) covalent geometry : angle 0.46071 ( 9100) hydrogen bonds : bond 0.04798 ( 537) hydrogen bonds : angle 4.01052 ( 1605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.219 Fit side-chains REVERT: A 376 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7845 (tp) REVERT: B 317 MET cc_start: 0.9146 (ttp) cc_final: 0.8724 (ttt) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.0801 time to fit residues: 9.6750 Evaluate side-chains 85 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 388 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.107670 restraints weight = 6931.232| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.26 r_work: 0.2913 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6686 Z= 0.136 Angle : 0.458 7.349 9100 Z= 0.240 Chirality : 0.039 0.169 1003 Planarity : 0.004 0.045 1107 Dihedral : 9.142 148.912 954 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.36 % Allowed : 8.91 % Favored : 89.73 % 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 aren not related in a simple way. whole: 2.88 (0.28), residues: 780 helix: 2.39 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR A 316 PHE 0.025 0.001 PHE A 26 TRP 0.019 0.001 TRP B 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6686) covalent geometry : angle 0.45754 ( 9100) hydrogen bonds : bond 0.04688 ( 537) hydrogen bonds : angle 3.97417 ( 1605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.241 Fit side-chains REVERT: A 376 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7849 (tp) REVERT: B 317 MET cc_start: 0.9149 (ttp) cc_final: 0.8733 (ttt) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.0861 time to fit residues: 10.6042 Evaluate side-chains 88 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.133838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.107348 restraints weight = 6898.184| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.25 r_work: 0.2934 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6686 Z= 0.136 Angle : 0.464 7.299 9100 Z= 0.244 Chirality : 0.039 0.176 1003 Planarity : 0.004 0.045 1107 Dihedral : 8.627 137.741 954 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.91 % Allowed : 9.37 % Favored : 89.73 % 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 aren not related in a simple way. whole: 2.90 (0.28), residues: 780 helix: 2.41 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.013 0.001 PHE A 164 TRP 0.019 0.001 TRP B 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6686) covalent geometry : angle 0.46418 ( 9100) hydrogen bonds : bond 0.04687 ( 537) hydrogen bonds : angle 3.95558 ( 1605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.246 Fit side-chains REVERT: A 376 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 299 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7311 (ttm110) REVERT: B 317 MET cc_start: 0.9130 (ttp) cc_final: 0.8702 (ttt) outliers start: 6 outliers final: 5 residues processed: 90 average time/residue: 0.0841 time to fit residues: 10.2345 Evaluate side-chains 89 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108296 restraints weight = 6834.633| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.33 r_work: 0.2951 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6686 Z= 0.138 Angle : 0.469 8.577 9100 Z= 0.244 Chirality : 0.039 0.204 1003 Planarity : 0.004 0.045 1107 Dihedral : 8.368 131.737 954 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.91 % Allowed : 9.67 % Favored : 89.43 % 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 aren not related in a simple way. whole: 2.91 (0.28), residues: 780 helix: 2.41 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.52), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.017 0.001 PHE A 26 TRP 0.021 0.001 TRP A 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6686) covalent geometry : angle 0.46857 ( 9100) hydrogen bonds : bond 0.04693 ( 537) hydrogen bonds : angle 3.94033 ( 1605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.203 Fit side-chains REVERT: A 376 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 299 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7318 (ttm110) REVERT: B 317 MET cc_start: 0.9127 (ttp) cc_final: 0.8694 (ttt) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.0810 time to fit residues: 9.3160 Evaluate side-chains 87 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain B residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.108476 restraints weight = 6938.302| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.25 r_work: 0.2910 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6686 Z= 0.140 Angle : 0.470 7.851 9100 Z= 0.245 Chirality : 0.039 0.204 1003 Planarity : 0.004 0.045 1107 Dihedral : 8.251 128.589 954 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.91 % Allowed : 9.82 % Favored : 89.27 % 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 aren not related in a simple way. whole: 2.91 (0.28), residues: 780 helix: 2.41 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 82 TYR 0.009 0.001 TYR A 116 PHE 0.016 0.001 PHE A 26 TRP 0.021 0.001 TRP B 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6686) covalent geometry : angle 0.47004 ( 9100) hydrogen bonds : bond 0.04704 ( 537) hydrogen bonds : angle 3.94527 ( 1605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.277 Fit side-chains REVERT: A 376 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7875 (tp) REVERT: B 317 MET cc_start: 0.9158 (ttp) cc_final: 0.8751 (ttt) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.0786 time to fit residues: 8.7424 Evaluate side-chains 85 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108580 restraints weight = 6886.931| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.30 r_work: 0.2942 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6686 Z= 0.126 Angle : 0.466 10.680 9100 Z= 0.241 Chirality : 0.039 0.250 1003 Planarity : 0.004 0.045 1107 Dihedral : 7.925 124.784 954 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.76 % Allowed : 10.27 % Favored : 88.97 % 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 aren not related in a simple way. whole: 3.01 (0.28), residues: 780 helix: 2.51 (0.19), residues: 654 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR B 116 PHE 0.015 0.001 PHE A 26 TRP 0.021 0.001 TRP A 34 HIS 0.002 0.000 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6686) covalent geometry : angle 0.46621 ( 9100) hydrogen bonds : bond 0.04504 ( 537) hydrogen bonds : angle 3.88867 ( 1605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.156 Fit side-chains REVERT: A 376 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7782 (tp) REVERT: B 299 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7259 (ttm110) REVERT: B 317 MET cc_start: 0.9111 (ttp) cc_final: 0.8680 (ttt) outliers start: 5 outliers final: 4 residues processed: 83 average time/residue: 0.0757 time to fit residues: 8.5618 Evaluate side-chains 84 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 352 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** B 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.135565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.108576 restraints weight = 6923.865| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.31 r_work: 0.2940 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6686 Z= 0.118 Angle : 0.455 9.223 9100 Z= 0.236 Chirality : 0.039 0.223 1003 Planarity : 0.004 0.046 1107 Dihedral : 7.601 120.140 954 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.60 % Allowed : 10.12 % Favored : 89.27 % 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 aren not related in a simple way. whole: 3.12 (0.28), residues: 780 helix: 2.58 (0.19), residues: 655 sheet: None (None), residues: 0 loop : -0.88 (0.50), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.009 0.001 TYR A 116 PHE 0.016 0.001 PHE A 26 TRP 0.021 0.001 TRP B 34 HIS 0.002 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6686) covalent geometry : angle 0.45542 ( 9100) hydrogen bonds : bond 0.04356 ( 537) hydrogen bonds : angle 3.82706 ( 1605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.96 seconds wall clock time: 26 minutes 35.56 seconds (1595.56 seconds total)