Starting phenix.real_space_refine on Thu Jul 2 05:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.cif Found real_map, /net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.map" model { file = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8in8_35592/07_2026/8in8_35592.cif" } resolution = 3.0 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= 0.072 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 4098 2.51 5 N 1140 2.21 5 O 1355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6663 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2009 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 244} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3685 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 441} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 21} Chain: "J" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 462 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.23, per 1000 atoms: 0.18 Number of scatterers: 6663 At special positions: 0 Unit cell: (71.6214, 87.0336, 107.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 47 15.00 Mg 1 11.99 O 1355 8.00 N 1140 7.00 C 4098 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: 0.37 Conformation dependent library (CDL) restraints added in 230.3 milliseconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 36.0% alpha, 20.7% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 356 through 367 Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.604A pdb=" N ILE B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 414 Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.694A pdb=" N LYS B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.616A pdb=" N ALA B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.688A pdb=" N ARG B 516 " --> pdb=" O PRO B 513 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU B 518 " --> pdb=" O ASP B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 Processing helix chain 'B' and resid 532 through 549 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.693A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 111 through 120 removed outlier: 4.191A pdb=" N GLY C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 151 through 157 removed outlier: 4.931A pdb=" N LYS C 156 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.736A pdb=" N LEU C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 208 removed outlier: 4.008A pdb=" N VAL C 196 " --> pdb=" O CYS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 295 removed outlier: 3.542A pdb=" N LYS C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 418 through 430 removed outlier: 3.872A pdb=" N LYS C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 470 through 473 removed outlier: 3.997A pdb=" N MET C 473 " --> pdb=" O ARG C 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 470 through 473' Processing sheet with id=AA1, first strand: chain 'B' and resid 579 through 581 removed outlier: 3.812A pdb=" N ALA C 355 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 335 through 337 removed outlier: 4.098A pdb=" N HIS B 444 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 335 through 337 Processing sheet with id=AA4, first strand: chain 'B' and resid 371 through 373 removed outlier: 3.819A pdb=" N VAL B 378 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 556 through 561 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.939A pdb=" N CYS C 107 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 56 " --> pdb=" O CYS C 107 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA C 53 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N TYR C 149 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 55 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 160 removed outlier: 3.550A pdb=" N TYR C 160 " --> pdb=" O PHE C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 307 removed outlier: 4.151A pdb=" N TYR C 224 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR C 467 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AB3, first strand: chain 'C' and resid 381 through 382 255 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1657 1.33 - 1.45: 1554 1.45 - 1.57: 3578 1.57 - 1.69: 92 1.69 - 1.81: 32 Bond restraints: 6913 Sorted by residual: bond pdb=" C3' DA J 18 " pdb=" C2' DA J 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.46e+00 bond pdb=" C3' DA J 1 " pdb=" C2' DA J 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.35e+00 bond pdb=" C3' DT J 17 " pdb=" C2' DT J 17 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.69e+00 bond pdb=" C3' DT J 6 " pdb=" C2' DT J 6 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 bond pdb=" C3' DC J 2 " pdb=" C2' DC J 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.57e+00 ... (remaining 6908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 9481 2.52 - 5.04: 93 5.04 - 7.55: 10 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 9586 Sorted by residual: angle pdb=" N3 DT J 6 " pdb=" C4 DT J 6 " pdb=" O4 DT J 6 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT J 17 " pdb=" C4 DT J 17 " pdb=" O4 DT J 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT J 4 " pdb=" C4 DT J 4 " pdb=" O4 DT J 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT J 16 " pdb=" C4 DT J 16 " pdb=" O4 DT J 16 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" O4 DT J 6 " pdb=" C4 DT J 6 " pdb=" C5 DT J 6 " ideal model delta sigma weight residual 124.90 122.18 2.72 7.00e-01 2.04e+00 1.51e+01 ... (remaining 9581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 3777 35.12 - 70.25: 242 70.25 - 105.37: 12 105.37 - 140.50: 1 140.50 - 175.62: 3 Dihedral angle restraints: 4035 sinusoidal: 1932 harmonic: 2103 Sorted by residual: dihedral pdb=" CA PHE B 328 " pdb=" C PHE B 328 " pdb=" N PRO B 329 " pdb=" CA PRO B 329 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL C 463 " pdb=" C VAL C 463 " pdb=" N ASN C 464 " pdb=" CA ASN C 464 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ILE C 14 " pdb=" C ILE C 14 " pdb=" N PRO C 15 " pdb=" CA PRO C 15 " ideal model delta harmonic sigma weight residual 180.00 -157.56 -22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 4032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 698 0.032 - 0.063: 252 0.063 - 0.094: 79 0.094 - 0.126: 46 0.126 - 0.157: 11 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C3' DC J -1 " pdb=" C4' DC J -1 " pdb=" O3' DC J -1 " pdb=" C2' DC J -1 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" C1' G I 7 " pdb=" O4' G I 7 " pdb=" C2' G I 7 " pdb=" N9 G I 7 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE C 407 " pdb=" N ILE C 407 " pdb=" C ILE C 407 " pdb=" CB ILE C 407 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1083 not shown) Planarity restraints: 1063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 272 " 0.058 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO C 273 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 273 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 273 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 56 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 57 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U I 5 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 U I 5 " -0.026 2.00e-02 2.50e+03 pdb=" C2 U I 5 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U I 5 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U I 5 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 5 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U I 5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U I 5 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I 5 " -0.005 2.00e-02 2.50e+03 ... (remaining 1060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 43 2.54 - 3.13: 4720 3.13 - 3.72: 10334 3.72 - 4.31: 14501 4.31 - 4.90: 23667 Nonbonded interactions: 53265 Sorted by model distance: nonbonded pdb=" OP1 A I 1 " pdb="MG MG I 101 " model vdw 1.950 2.170 nonbonded pdb=" OP3 A I 1 " pdb="MG MG I 101 " model vdw 2.001 2.170 nonbonded pdb=" O MET C 473 " pdb="MG MG I 101 " model vdw 2.015 2.170 nonbonded pdb=" O GLN C 281 " pdb=" OG SER C 285 " model vdw 2.225 3.040 nonbonded pdb=" O LEU C 426 " pdb=" OG1 THR C 429 " model vdw 2.233 3.040 ... (remaining 53260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 5.890 Find NCS groups from input model: 0.020 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:5.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 0.046 6913 Z= 0.239 Angle : 0.637 12.588 9586 Z= 0.384 Chirality : 0.042 0.157 1086 Planarity : 0.005 0.086 1063 Dihedral : 20.421 175.621 2683 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Rotamer: Outliers : 3.63 % Allowed : 33.50 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.30 (0.32), residues: 718 helix: 1.49 (0.37), residues: 211 sheet: -0.16 (0.44), residues: 160 loop : -1.30 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 62 TYR 0.013 0.001 TYR C 469 PHE 0.010 0.001 PHE C 158 TRP 0.007 0.001 TRP B 502 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.24 ( 6913) covalent geometry : angle 0.63712 / 0.38 ( 9586) hydrogen bonds : bond 0.14572 / 10.35 ( 281) hydrogen bonds : angle 6.32515 / 4.29 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.138 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 21 residues processed: 75 average time/residue: 0.3109 time to fit residues: 24.9836 Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 575 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 358 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131197 restraints weight = 7863.508| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.94 r_work: 0.3657 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6913 Z= 0.139 Angle : 0.590 8.277 9586 Z= 0.321 Chirality : 0.042 0.249 1086 Planarity : 0.005 0.056 1063 Dihedral : 17.118 177.185 1369 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.45 % Allowed : 29.87 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.22 (0.32), residues: 718 helix: 1.48 (0.36), residues: 224 sheet: 0.01 (0.44), residues: 156 loop : -1.37 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.012 0.001 TYR C 341 PHE 0.007 0.001 PHE B 523 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 6913) covalent geometry : angle 0.58982 / 0.32 ( 9586) hydrogen bonds : bond 0.04346 / 2.88 ( 281) hydrogen bonds : angle 4.94540 / 3.39 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7971 (m-30) cc_final: 0.7767 (m-30) outliers start: 33 outliers final: 17 residues processed: 86 average time/residue: 0.3204 time to fit residues: 29.6285 Evaluate side-chains 71 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.163624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132189 restraints weight = 7833.457| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.94 r_work: 0.3673 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6913 Z= 0.123 Angle : 0.566 9.136 9586 Z= 0.307 Chirality : 0.041 0.258 1086 Planarity : 0.004 0.050 1063 Dihedral : 17.000 174.685 1359 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.95 % Allowed : 31.52 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 718 helix: 1.60 (0.35), residues: 224 sheet: 0.15 (0.44), residues: 155 loop : -1.39 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.010 0.001 TYR B 537 PHE 0.007 0.001 PHE C 452 TRP 0.006 0.001 TRP B 502 HIS 0.003 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6913) covalent geometry : angle 0.56628 / 0.31 ( 9586) hydrogen bonds : bond 0.03903 / 2.58 ( 281) hydrogen bonds : angle 4.69189 / 3.21 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7996 (m-30) cc_final: 0.7702 (m-30) outliers start: 30 outliers final: 12 residues processed: 88 average time/residue: 0.3133 time to fit residues: 29.7587 Evaluate side-chains 70 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.159480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128049 restraints weight = 7952.254| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.94 r_work: 0.3568 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6913 Z= 0.225 Angle : 0.662 6.859 9586 Z= 0.356 Chirality : 0.047 0.257 1086 Planarity : 0.006 0.060 1063 Dihedral : 17.118 176.066 1352 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.82 % Favored : 93.04 % Rotamer: Outliers : 6.11 % Allowed : 31.19 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.64 (0.31), residues: 718 helix: 1.00 (0.35), residues: 224 sheet: -0.18 (0.43), residues: 160 loop : -1.56 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 62 TYR 0.026 0.002 TYR C 341 PHE 0.014 0.002 PHE C 143 TRP 0.010 0.002 TRP C 377 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 6913) covalent geometry : angle 0.66188 / 0.36 ( 9586) hydrogen bonds : bond 0.05179 / 3.47 ( 281) hydrogen bonds : angle 4.91594 / 3.39 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.7973 (m-30) cc_final: 0.7662 (m-30) outliers start: 37 outliers final: 13 residues processed: 95 average time/residue: 0.3802 time to fit residues: 38.5790 Evaluate side-chains 78 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 42 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 64 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128825 restraints weight = 8004.423| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.97 r_work: 0.3623 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6913 Z= 0.127 Angle : 0.581 7.117 9586 Z= 0.317 Chirality : 0.043 0.255 1086 Planarity : 0.005 0.057 1063 Dihedral : 17.035 175.706 1351 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.79 % Allowed : 32.34 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.30 (0.32), residues: 718 helix: 1.44 (0.36), residues: 224 sheet: -0.05 (0.43), residues: 159 loop : -1.45 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 62 TYR 0.013 0.001 TYR C 260 PHE 0.007 0.001 PHE C 158 TRP 0.007 0.001 TRP C 198 HIS 0.002 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 6913) covalent geometry : angle 0.58070 / 0.32 ( 9586) hydrogen bonds : bond 0.03847 / 2.53 ( 281) hydrogen bonds : angle 4.68073 / 3.22 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6287 (tptp) REVERT: B 455 ASP cc_start: 0.7970 (m-30) cc_final: 0.7619 (m-30) REVERT: C 260 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6473 (p90) outliers start: 29 outliers final: 10 residues processed: 88 average time/residue: 0.3942 time to fit residues: 36.8374 Evaluate side-chains 73 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.158804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.127121 restraints weight = 7969.944| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.95 r_work: 0.3610 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6913 Z= 0.149 Angle : 0.604 8.002 9586 Z= 0.327 Chirality : 0.043 0.255 1086 Planarity : 0.005 0.060 1063 Dihedral : 17.003 175.727 1351 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.80 % Allowed : 33.33 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.39 (0.32), residues: 718 helix: 1.34 (0.36), residues: 224 sheet: -0.14 (0.43), residues: 162 loop : -1.45 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 62 TYR 0.016 0.001 TYR C 341 PHE 0.008 0.001 PHE C 471 TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6913) covalent geometry : angle 0.60395 / 0.33 ( 9586) hydrogen bonds : bond 0.04000 / 2.64 ( 281) hydrogen bonds : angle 4.64382 / 3.20 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6319 (tptp) REVERT: B 455 ASP cc_start: 0.7954 (m-30) cc_final: 0.7602 (m-30) REVERT: B 508 GLU cc_start: 0.7709 (mp0) cc_final: 0.7474 (mt-10) REVERT: B 528 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7263 (ttt-90) REVERT: C 260 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.6871 (p90) outliers start: 23 outliers final: 11 residues processed: 83 average time/residue: 0.3934 time to fit residues: 34.6879 Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 chunk 14 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.155376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123755 restraints weight = 7977.013| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.92 r_work: 0.3553 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6913 Z= 0.237 Angle : 0.701 7.085 9586 Z= 0.375 Chirality : 0.049 0.262 1086 Planarity : 0.006 0.064 1063 Dihedral : 17.128 176.373 1351 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 5.12 % Allowed : 32.34 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.81 (0.31), residues: 718 helix: 0.76 (0.35), residues: 223 sheet: -0.01 (0.43), residues: 156 loop : -1.71 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 62 TYR 0.032 0.003 TYR C 341 PHE 0.015 0.002 PHE C 143 TRP 0.010 0.002 TRP C 377 HIS 0.004 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 ( 6913) covalent geometry : angle 0.70076 / 0.37 ( 9586) hydrogen bonds : bond 0.05230 / 3.50 ( 281) hydrogen bonds : angle 4.92596 / 3.42 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6479 (tptp) REVERT: B 455 ASP cc_start: 0.7950 (m-30) cc_final: 0.7626 (m-30) REVERT: C 130 VAL cc_start: 0.7655 (t) cc_final: 0.7368 (p) REVERT: C 260 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7136 (p90) REVERT: C 352 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.5988 (tttt) outliers start: 31 outliers final: 18 residues processed: 90 average time/residue: 0.4026 time to fit residues: 38.5107 Evaluate side-chains 82 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 260 TYR Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 2.9990 chunk 70 optimal weight: 0.0670 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 558 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.127770 restraints weight = 7969.903| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.95 r_work: 0.3626 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6913 Z= 0.141 Angle : 0.633 9.077 9586 Z= 0.339 Chirality : 0.044 0.259 1086 Planarity : 0.005 0.062 1063 Dihedral : 17.097 175.849 1351 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.81 % Allowed : 34.65 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.47 (0.32), residues: 718 helix: 1.23 (0.36), residues: 223 sheet: 0.13 (0.45), residues: 151 loop : -1.60 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 62 TYR 0.013 0.001 TYR B 537 PHE 0.008 0.001 PHE C 158 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS B 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6913) covalent geometry : angle 0.63348 / 0.34 ( 9586) hydrogen bonds : bond 0.03845 / 2.54 ( 281) hydrogen bonds : angle 4.67721 / 3.22 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.6316 (tptp) REVERT: B 455 ASP cc_start: 0.7919 (m-30) cc_final: 0.7541 (m-30) REVERT: B 508 GLU cc_start: 0.7688 (mp0) cc_final: 0.7339 (mt-10) REVERT: C 130 VAL cc_start: 0.7711 (t) cc_final: 0.7421 (p) REVERT: C 352 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6093 (tttt) outliers start: 17 outliers final: 13 residues processed: 79 average time/residue: 0.4495 time to fit residues: 37.6056 Evaluate side-chains 76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 462 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.0060 overall best weight: 1.0400 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.158837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126946 restraints weight = 7987.634| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.95 r_work: 0.3605 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6913 Z= 0.147 Angle : 0.622 7.701 9586 Z= 0.335 Chirality : 0.044 0.259 1086 Planarity : 0.005 0.064 1063 Dihedral : 17.041 175.921 1349 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.14 % Allowed : 34.32 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.43 (0.32), residues: 718 helix: 1.25 (0.36), residues: 223 sheet: -0.01 (0.44), residues: 158 loop : -1.51 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 263 TYR 0.016 0.001 TYR C 341 PHE 0.008 0.001 PHE C 471 TRP 0.007 0.001 TRP C 377 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 6913) covalent geometry : angle 0.62199 / 0.33 ( 9586) hydrogen bonds : bond 0.03972 / 2.64 ( 281) hydrogen bonds : angle 4.60873 / 3.17 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6345 (tptp) REVERT: B 455 ASP cc_start: 0.7927 (m-30) cc_final: 0.7581 (m-30) REVERT: C 352 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.5941 (tttt) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.4229 time to fit residues: 34.9687 Evaluate side-chains 76 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 59 optimal weight: 0.0040 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130970 restraints weight = 7930.787| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.95 r_work: 0.3657 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6913 Z= 0.124 Angle : 0.608 7.825 9586 Z= 0.328 Chirality : 0.042 0.255 1086 Planarity : 0.005 0.063 1063 Dihedral : 17.009 176.023 1349 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.82 % Allowed : 35.97 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.23 (0.32), residues: 718 helix: 1.37 (0.35), residues: 226 sheet: 0.08 (0.44), residues: 160 loop : -1.37 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 263 TYR 0.013 0.001 TYR C 54 PHE 0.012 0.001 PHE B 523 TRP 0.009 0.001 TRP B 502 HIS 0.003 0.001 HIS C 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6913) covalent geometry : angle 0.60841 / 0.33 ( 9586) hydrogen bonds : bond 0.03454 / 2.28 ( 281) hydrogen bonds : angle 4.47036 / 3.06 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: B 418 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6209 (tptp) REVERT: B 455 ASP cc_start: 0.7932 (m-30) cc_final: 0.7547 (m-30) REVERT: B 508 GLU cc_start: 0.7604 (mp0) cc_final: 0.7364 (mt-10) REVERT: C 119 ASN cc_start: 0.7438 (p0) cc_final: 0.6755 (m110) REVERT: C 280 MET cc_start: 0.7164 (mmt) cc_final: 0.6931 (mmm) REVERT: C 346 ASP cc_start: 0.7858 (m-30) cc_final: 0.6886 (t0) outliers start: 11 outliers final: 10 residues processed: 72 average time/residue: 0.4300 time to fit residues: 32.7295 Evaluate side-chains 70 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 407 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 overall best weight: 0.5552 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.166278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.135488 restraints weight = 7790.494| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.90 r_work: 0.3720 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6913 Z= 0.126 Angle : 0.610 8.458 9586 Z= 0.326 Chirality : 0.042 0.255 1086 Planarity : 0.005 0.065 1063 Dihedral : 16.972 176.178 1349 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.82 % Allowed : 36.30 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 718 helix: 1.44 (0.35), residues: 226 sheet: 0.12 (0.43), residues: 166 loop : -1.30 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 263 TYR 0.016 0.001 TYR C 469 PHE 0.007 0.001 PHE B 523 TRP 0.008 0.001 TRP B 502 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6913) covalent geometry : angle 0.60989 / 0.33 ( 9586) hydrogen bonds : bond 0.03507 / 2.34 ( 281) hydrogen bonds : angle 4.38824 / 3.00 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.88 seconds wall clock time: 33 minutes 22.84 seconds (2002.84 seconds total)