Starting phenix.real_space_refine on Tue Mar 3 19:22:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2026/7ozw_13139.map" } resolution = 3.38 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= 0.020 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 34 5.49 5 S 14 5.16 5 C 5341 2.51 5 N 1404 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8407 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4388 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 514} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3303 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 379} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 699 Classifications: {'DNA': 32, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 33} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'3IR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.28 Number of scatterers: 8407 At special positions: 0 Unit cell: (94.09, 99.91, 102.82, 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 14 16.00 P 34 15.00 O 1614 8.00 N 1404 7.00 C 5341 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: 0.85 Conformation dependent library (CDL) restraints added in 304.6 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.8% alpha, 14.2% beta 11 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.955A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.172A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.716A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.646A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.524A pdb=" N THR A 377 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.550A pdb=" N SER A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.753A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 127 removed outlier: 4.688A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.984A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.633A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.544A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.946A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 removed outlier: 3.695A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 removed outlier: 3.545A pdb=" N TYR A 183 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.730A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.353A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.716A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.793A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.531A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.803A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.906A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 350 through 355 removed outlier: 3.635A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1323 1.32 - 1.44: 2426 1.44 - 1.56: 4858 1.56 - 1.69: 68 1.69 - 1.81: 26 Bond restraints: 8701 Sorted by residual: bond pdb=" C4' DC F 10 " pdb=" O4' DC F 10 " ideal model delta sigma weight residual 1.450 1.555 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C5 3IR A 601 " pdb=" C7 3IR A 601 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 3IR A 601 " pdb=" C5 3IR A 601 " ideal model delta sigma weight residual 1.483 1.585 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3' DG F 31 " pdb=" P DG F 32 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.50e-02 4.44e+03 2.27e+01 bond pdb=" C1 3IR A 601 " pdb=" N1 3IR A 601 " ideal model delta sigma weight residual 1.373 1.465 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 11935 4.42 - 8.84: 52 8.84 - 13.26: 2 13.26 - 17.68: 1 17.68 - 22.11: 1 Bond angle restraints: 11991 Sorted by residual: angle pdb=" C5' DC F 10 " pdb=" C4' DC F 10 " pdb=" O4' DC F 10 " ideal model delta sigma weight residual 109.40 131.51 -22.11 1.50e+00 4.44e-01 2.17e+02 angle pdb=" C5 3IR A 601 " pdb=" C7 3IR A 601 " pdb=" C8 3IR A 601 " ideal model delta sigma weight residual 120.05 136.38 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 106.61 115.90 -9.29 1.78e+00 3.16e-01 2.73e+01 angle pdb=" C5' DG F 24 " pdb=" C4' DG F 24 " pdb=" O4' DG F 24 " ideal model delta sigma weight residual 109.40 116.21 -6.81 1.50e+00 4.44e-01 2.06e+01 angle pdb=" N TRP A 535 " pdb=" CA TRP A 535 " pdb=" C TRP A 535 " ideal model delta sigma weight residual 109.07 116.26 -7.19 1.61e+00 3.86e-01 1.99e+01 ... (remaining 11986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4391 17.89 - 35.77: 509 35.77 - 53.66: 143 53.66 - 71.55: 36 71.55 - 89.43: 9 Dihedral angle restraints: 5088 sinusoidal: 2281 harmonic: 2807 Sorted by residual: dihedral pdb=" CA VAL B 423 " pdb=" C VAL B 423 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA VAL A 35 " pdb=" C VAL A 35 " pdb=" N GLU A 36 " pdb=" CA GLU A 36 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASP B 86 " pdb=" C ASP B 86 " pdb=" N PHE B 87 " pdb=" CA PHE B 87 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1303 0.152 - 0.305: 14 0.305 - 0.457: 2 0.457 - 0.609: 0 0.609 - 0.762: 1 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C4' DC F 10 " pdb=" C5' DC F 10 " pdb=" O4' DC F 10 " pdb=" C3' DC F 10 " both_signs ideal model delta sigma weight residual False -2.53 -1.76 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" CA PHE B 77 " pdb=" N PHE B 77 " pdb=" C PHE B 77 " pdb=" CB PHE B 77 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C4' DG F 24 " pdb=" C5' DG F 24 " pdb=" O4' DG F 24 " pdb=" C3' DG F 24 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1317 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 312 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 313 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 125 " -0.205 9.50e-02 1.11e+02 9.20e-02 5.20e+00 pdb=" NE ARG B 125 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 125 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 125 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 125 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " 0.011 2.00e-02 2.50e+03 1.11e-02 3.08e+00 pdb=" CG TRP B 414 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.002 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2069 2.80 - 3.33: 7487 3.33 - 3.85: 14044 3.85 - 4.38: 16326 4.38 - 4.90: 27492 Nonbonded interactions: 67418 Sorted by model distance: nonbonded pdb=" NH1 ARG A 277 " pdb=" O ALA A 355 " model vdw 2.276 3.120 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.308 3.120 nonbonded pdb=" O TYR A 427 " pdb=" NE2 GLN A 509 " model vdw 2.323 3.120 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.328 3.120 nonbonded pdb=" OG1 THR A 403 " pdb=" OE1 GLU A 404 " model vdw 2.329 3.040 ... (remaining 67413 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: 0.200 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 8701 Z= 0.256 Angle : 0.838 22.106 11991 Z= 0.480 Chirality : 0.055 0.762 1320 Planarity : 0.005 0.092 1395 Dihedral : 16.830 89.432 3278 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.27), residues: 955 helix: 0.76 (0.29), residues: 326 sheet: 0.00 (0.42), residues: 126 loop : -0.83 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 358 TYR 0.017 0.001 TYR A 532 PHE 0.010 0.001 PHE A 160 TRP 0.029 0.001 TRP B 414 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 8701) covalent geometry : angle 0.83758 (11991) hydrogen bonds : bond 0.17032 ( 343) hydrogen bonds : angle 7.85879 ( 928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 287 LYS cc_start: 0.7461 (mppt) cc_final: 0.7113 (mmtp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1172 time to fit residues: 19.0046 Evaluate side-chains 101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.208791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166519 restraints weight = 9497.685| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.81 r_work: 0.3773 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8701 Z= 0.208 Angle : 0.660 8.960 11991 Z= 0.344 Chirality : 0.045 0.148 1320 Planarity : 0.005 0.061 1395 Dihedral : 16.241 82.607 1375 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.61 % Allowed : 7.62 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.27), residues: 955 helix: 0.89 (0.29), residues: 326 sheet: -0.61 (0.39), residues: 142 loop : -0.73 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 143 TYR 0.018 0.002 TYR B 181 PHE 0.017 0.002 PHE B 130 TRP 0.018 0.002 TRP A 402 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8701) covalent geometry : angle 0.65970 (11991) hydrogen bonds : bond 0.04879 ( 343) hydrogen bonds : angle 5.26728 ( 928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.7626 (ptm) cc_final: 0.7314 (ptm) REVERT: A 476 LYS cc_start: 0.6444 (mptt) cc_final: 0.5588 (mttt) REVERT: B 194 GLU cc_start: 0.6506 (pm20) cc_final: 0.6152 (tm-30) REVERT: B 201 LYS cc_start: 0.7251 (tttt) cc_final: 0.6992 (tttm) REVERT: B 342 TYR cc_start: 0.7731 (p90) cc_final: 0.7317 (p90) outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.1062 time to fit residues: 16.5311 Evaluate side-chains 105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 84 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 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 = 0.4396 r_free = 0.4396 target = 0.210466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.170709 restraints weight = 9330.811| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.88 r_work: 0.3793 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8701 Z= 0.153 Angle : 0.595 8.038 11991 Z= 0.309 Chirality : 0.043 0.144 1320 Planarity : 0.005 0.055 1395 Dihedral : 16.174 82.433 1375 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.11 % Allowed : 10.81 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 955 helix: 1.16 (0.29), residues: 325 sheet: -0.74 (0.39), residues: 142 loop : -0.70 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.013 0.002 TYR B 181 PHE 0.014 0.001 PHE B 130 TRP 0.021 0.001 TRP A 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8701) covalent geometry : angle 0.59479 (11991) hydrogen bonds : bond 0.04126 ( 343) hydrogen bonds : angle 4.94385 ( 928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.310 Fit side-chains REVERT: A 145 GLN cc_start: 0.7915 (pp30) cc_final: 0.7281 (pp30) REVERT: A 184 MET cc_start: 0.6543 (mmt) cc_final: 0.6208 (tpt) REVERT: A 373 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 469 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6700 (mp) REVERT: A 551 LEU cc_start: 0.5337 (mp) cc_final: 0.5021 (mt) REVERT: B 342 TYR cc_start: 0.7469 (p90) cc_final: 0.7106 (p90) outliers start: 9 outliers final: 7 residues processed: 124 average time/residue: 0.0989 time to fit residues: 17.0145 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN A 428 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.206280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166155 restraints weight = 9564.477| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.86 r_work: 0.3756 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8701 Z= 0.199 Angle : 0.633 8.111 11991 Z= 0.330 Chirality : 0.044 0.145 1320 Planarity : 0.005 0.053 1395 Dihedral : 16.194 82.429 1375 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.47 % Allowed : 13.39 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 955 helix: 0.90 (0.29), residues: 327 sheet: -0.91 (0.39), residues: 143 loop : -0.81 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.015 0.002 TYR A 181 PHE 0.016 0.002 PHE B 130 TRP 0.025 0.002 TRP A 402 HIS 0.007 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8701) covalent geometry : angle 0.63288 (11991) hydrogen bonds : bond 0.04424 ( 343) hydrogen bonds : angle 5.00725 ( 928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.299 Fit side-chains REVERT: A 31 ILE cc_start: 0.5283 (pt) cc_final: 0.4960 (pt) REVERT: A 145 GLN cc_start: 0.7986 (pp30) cc_final: 0.7291 (pp30) REVERT: A 184 MET cc_start: 0.6861 (mmt) cc_final: 0.6560 (tpt) REVERT: A 269 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: A 469 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6859 (mp) REVERT: B 342 TYR cc_start: 0.7587 (p90) cc_final: 0.7203 (p90) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.0992 time to fit residues: 16.7208 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** 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 = 0.4407 r_free = 0.4407 target = 0.211152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170882 restraints weight = 9438.468| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.79 r_work: 0.3808 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8701 Z= 0.130 Angle : 0.584 7.495 11991 Z= 0.304 Chirality : 0.042 0.142 1320 Planarity : 0.004 0.050 1395 Dihedral : 16.025 82.397 1375 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.23 % Allowed : 15.48 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.04 (0.27), residues: 955 helix: 1.32 (0.30), residues: 326 sheet: -0.74 (0.40), residues: 138 loop : -0.71 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.012 0.001 TYR A 232 PHE 0.013 0.001 PHE B 130 TRP 0.024 0.001 TRP A 402 HIS 0.003 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8701) covalent geometry : angle 0.58440 (11991) hydrogen bonds : bond 0.03664 ( 343) hydrogen bonds : angle 4.85642 ( 928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7960 (pp30) cc_final: 0.7219 (pp30) REVERT: A 184 MET cc_start: 0.6820 (mmt) cc_final: 0.6529 (tpt) REVERT: A 232 TYR cc_start: 0.7763 (m-10) cc_final: 0.7404 (m-10) REVERT: A 269 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6865 (mp10) REVERT: B 342 TYR cc_start: 0.7499 (p90) cc_final: 0.7126 (p90) outliers start: 10 outliers final: 6 residues processed: 127 average time/residue: 0.1004 time to fit residues: 17.5550 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.0040 chunk 68 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.210557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170489 restraints weight = 9297.544| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.76 r_work: 0.3793 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8701 Z= 0.144 Angle : 0.582 7.498 11991 Z= 0.302 Chirality : 0.042 0.140 1320 Planarity : 0.004 0.049 1395 Dihedral : 15.959 82.298 1375 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.47 % Allowed : 15.60 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.01 (0.28), residues: 955 helix: 1.34 (0.30), residues: 327 sheet: -0.63 (0.40), residues: 144 loop : -0.69 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 143 TYR 0.011 0.001 TYR A 181 PHE 0.013 0.001 PHE B 130 TRP 0.024 0.001 TRP A 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8701) covalent geometry : angle 0.58224 (11991) hydrogen bonds : bond 0.03741 ( 343) hydrogen bonds : angle 4.77833 ( 928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8066 (pp30) cc_final: 0.7622 (pp30) REVERT: A 184 MET cc_start: 0.6977 (mmt) cc_final: 0.6664 (tpt) REVERT: A 269 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: B 342 TYR cc_start: 0.7731 (p90) cc_final: 0.7391 (p90) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.1024 time to fit residues: 17.5181 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.207845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166682 restraints weight = 9497.535| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.80 r_work: 0.3770 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8701 Z= 0.198 Angle : 0.647 8.706 11991 Z= 0.335 Chirality : 0.044 0.147 1320 Planarity : 0.005 0.049 1395 Dihedral : 16.076 83.070 1375 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.72 % Allowed : 16.46 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.28 (0.27), residues: 955 helix: 1.08 (0.29), residues: 326 sheet: -0.85 (0.39), residues: 146 loop : -0.82 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.014 0.002 TYR A 181 PHE 0.016 0.002 PHE B 130 TRP 0.026 0.002 TRP A 402 HIS 0.006 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8701) covalent geometry : angle 0.64725 (11991) hydrogen bonds : bond 0.04193 ( 343) hydrogen bonds : angle 4.89009 ( 928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.382 Fit side-chains REVERT: A 79 GLU cc_start: 0.5552 (pm20) cc_final: 0.5324 (tp30) REVERT: A 184 MET cc_start: 0.7041 (mmt) cc_final: 0.6760 (tpt) REVERT: A 269 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 551 LEU cc_start: 0.5477 (mp) cc_final: 0.5207 (mt) REVERT: B 342 TYR cc_start: 0.7752 (p90) cc_final: 0.7440 (p90) outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 0.0941 time to fit residues: 15.4920 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.206513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.166034 restraints weight = 9376.155| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.76 r_work: 0.3740 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8701 Z= 0.228 Angle : 0.685 8.457 11991 Z= 0.356 Chirality : 0.045 0.155 1320 Planarity : 0.005 0.050 1395 Dihedral : 16.282 84.477 1375 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.60 % Allowed : 16.46 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.60 (0.27), residues: 955 helix: 0.73 (0.29), residues: 326 sheet: -0.97 (0.40), residues: 141 loop : -0.96 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.017 0.002 TYR A 181 PHE 0.017 0.002 PHE B 130 TRP 0.026 0.002 TRP A 402 HIS 0.007 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 8701) covalent geometry : angle 0.68495 (11991) hydrogen bonds : bond 0.04607 ( 343) hydrogen bonds : angle 5.03275 ( 928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.235 Fit side-chains REVERT: A 79 GLU cc_start: 0.5674 (pm20) cc_final: 0.5233 (tp30) REVERT: A 184 MET cc_start: 0.7151 (mmt) cc_final: 0.6838 (tpt) REVERT: A 269 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: A 551 LEU cc_start: 0.5228 (mp) cc_final: 0.4950 (mt) REVERT: B 342 TYR cc_start: 0.7773 (p90) cc_final: 0.7471 (p90) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.0942 time to fit residues: 15.5369 Evaluate side-chains 114 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 174 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.209129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169307 restraints weight = 9369.333| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.88 r_work: 0.3749 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8701 Z= 0.162 Angle : 0.630 9.447 11991 Z= 0.327 Chirality : 0.043 0.145 1320 Planarity : 0.005 0.048 1395 Dihedral : 16.165 85.581 1375 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.47 % Allowed : 16.95 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.40 (0.27), residues: 955 helix: 0.98 (0.29), residues: 326 sheet: -0.84 (0.40), residues: 145 loop : -0.92 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 143 TYR 0.013 0.002 TYR A 181 PHE 0.015 0.001 PHE B 130 TRP 0.035 0.002 TRP B 402 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8701) covalent geometry : angle 0.63046 (11991) hydrogen bonds : bond 0.04002 ( 343) hydrogen bonds : angle 4.94743 ( 928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.302 Fit side-chains REVERT: A 79 GLU cc_start: 0.5566 (pm20) cc_final: 0.5233 (tp30) REVERT: A 102 LYS cc_start: 0.6161 (mmmt) cc_final: 0.5858 (tppt) REVERT: A 184 MET cc_start: 0.6972 (mmt) cc_final: 0.6683 (tpt) REVERT: A 269 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: A 277 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6782 (mtp85) REVERT: A 358 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6714 (mmm160) REVERT: A 551 LEU cc_start: 0.5309 (mp) cc_final: 0.5073 (mt) REVERT: B 342 TYR cc_start: 0.7537 (p90) cc_final: 0.7265 (p90) outliers start: 12 outliers final: 10 residues processed: 123 average time/residue: 0.0966 time to fit residues: 16.4027 Evaluate side-chains 120 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.206517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167133 restraints weight = 9410.865| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.82 r_work: 0.3740 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8701 Z= 0.234 Angle : 0.695 9.934 11991 Z= 0.361 Chirality : 0.045 0.151 1320 Planarity : 0.005 0.049 1395 Dihedral : 16.308 86.154 1375 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.60 % Allowed : 17.08 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.70 (0.27), residues: 955 helix: 0.62 (0.29), residues: 326 sheet: -0.91 (0.41), residues: 139 loop : -1.05 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 143 TYR 0.017 0.002 TYR A 181 PHE 0.017 0.002 PHE B 130 TRP 0.028 0.002 TRP B 402 HIS 0.007 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8701) covalent geometry : angle 0.69480 (11991) hydrogen bonds : bond 0.04631 ( 343) hydrogen bonds : angle 5.09254 ( 928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.266 Fit side-chains REVERT: A 79 GLU cc_start: 0.5580 (pm20) cc_final: 0.5120 (tp30) REVERT: A 184 MET cc_start: 0.7054 (mmt) cc_final: 0.6734 (tpt) REVERT: A 269 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6975 (mp10) REVERT: A 277 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6813 (mtp85) REVERT: A 373 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8014 (tt0) REVERT: A 551 LEU cc_start: 0.5373 (mp) cc_final: 0.5113 (mt) REVERT: B 342 TYR cc_start: 0.7546 (p90) cc_final: 0.7260 (p90) outliers start: 13 outliers final: 10 residues processed: 115 average time/residue: 0.1079 time to fit residues: 16.8087 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.8980 chunk 6 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 88 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.213569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171910 restraints weight = 9257.310| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.76 r_work: 0.3853 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8701 Z= 0.116 Angle : 0.604 10.152 11991 Z= 0.312 Chirality : 0.042 0.152 1320 Planarity : 0.005 0.047 1395 Dihedral : 15.912 86.599 1375 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.98 % Allowed : 18.18 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.27), residues: 955 helix: 1.31 (0.30), residues: 325 sheet: -0.67 (0.42), residues: 139 loop : -0.84 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.022 0.001 TYR A 232 PHE 0.012 0.001 PHE A 160 TRP 0.024 0.001 TRP A 402 HIS 0.005 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8701) covalent geometry : angle 0.60387 (11991) hydrogen bonds : bond 0.03352 ( 343) hydrogen bonds : angle 4.87986 ( 928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.26 seconds wall clock time: 36 minutes 5.86 seconds (2165.86 seconds total)