Starting phenix.real_space_refine on Wed Mar 12 21:02:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_13139.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_13139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_13139.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_13139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozw_13139/03_2025/7ozw_13139.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: 5.00, per 1000 atoms: 0.59 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: 2.17 Conformation dependent library (CDL) restraints added in 870.0 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: 2.76 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: 2.54 Time building geometry restraints manager: 2.56 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- 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= 0.278 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 : 7.68 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.029 0.001 TRP B 414 HIS 0.003 0.001 HIS A 198 PHE 0.010 0.001 PHE A 160 TYR 0.017 0.001 TYR A 532 ARG 0.005 0.000 ARG A 358 *********************** 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 : 0.941 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: 0.2643 time to fit residues: 42.7411 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 : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0570 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 0.0470 chunk 39 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.217864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176914 restraints weight = 9227.642| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.78 r_work: 0.3905 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8701 Z= 0.154 Angle : 0.563 8.009 11991 Z= 0.292 Chirality : 0.042 0.135 1320 Planarity : 0.004 0.057 1395 Dihedral : 15.969 81.970 1375 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.25 % Allowed : 6.63 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 955 helix: 1.50 (0.30), residues: 326 sheet: -0.03 (0.41), residues: 130 loop : -0.54 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 402 HIS 0.002 0.001 HIS A 235 PHE 0.010 0.001 PHE A 160 TYR 0.012 0.001 TYR A 501 ARG 0.006 0.001 ARG A 143 *********************** 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 123 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.866 Fit side-chains REVERT: A 145 GLN cc_start: 0.7829 (pp30) cc_final: 0.7468 (pp30) REVERT: A 356 ARG cc_start: 0.8092 (ttt-90) cc_final: 0.7890 (ttt-90) REVERT: A 373 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 469 LEU cc_start: 0.7205 (tp) cc_final: 0.6866 (tp) REVERT: A 476 LYS cc_start: 0.6358 (mptt) cc_final: 0.5780 (mttt) REVERT: B 194 GLU cc_start: 0.6352 (pm20) cc_final: 0.6125 (tm-30) REVERT: B 198 HIS cc_start: 0.6870 (t70) cc_final: 0.6654 (t70) REVERT: B 342 TYR cc_start: 0.7540 (p90) cc_final: 0.7211 (p90) outliers start: 2 outliers final: 2 residues processed: 123 average time/residue: 0.2340 time to fit residues: 38.5806 Evaluate side-chains 107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 145 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 = 0.4376 r_free = 0.4376 target = 0.208096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168271 restraints weight = 9443.796| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 1.89 r_work: 0.3763 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1562 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= 0.345 Angle : 0.678 7.487 11991 Z= 0.354 Chirality : 0.046 0.147 1320 Planarity : 0.005 0.055 1395 Dihedral : 16.203 81.534 1375 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 9.95 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 955 helix: 1.03 (0.29), residues: 326 sheet: -0.71 (0.40), residues: 143 loop : -0.67 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 402 HIS 0.010 0.002 HIS A 198 PHE 0.017 0.002 PHE B 87 TYR 0.017 0.003 TYR B 181 ARG 0.008 0.001 ARG B 125 *********************** 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 121 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7998 (pp30) cc_final: 0.7392 (pp30) REVERT: A 476 LYS cc_start: 0.6403 (mptt) cc_final: 0.5639 (mttt) REVERT: A 551 LEU cc_start: 0.5148 (mp) cc_final: 0.4878 (mt) REVERT: B 342 TYR cc_start: 0.7611 (p90) cc_final: 0.7217 (p90) outliers start: 9 outliers final: 6 residues processed: 118 average time/residue: 0.2106 time to fit residues: 34.3278 Evaluate side-chains 111 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 269 GLN Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 30.0000 chunk 51 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.212313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171924 restraints weight = 9319.359| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.83 r_work: 0.3795 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8701 Z= 0.185 Angle : 0.565 7.376 11991 Z= 0.294 Chirality : 0.042 0.141 1320 Planarity : 0.004 0.052 1395 Dihedral : 15.912 81.363 1375 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.23 % Allowed : 12.29 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 955 helix: 1.38 (0.30), residues: 327 sheet: -0.69 (0.39), residues: 144 loop : -0.58 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 402 HIS 0.004 0.001 HIS A 198 PHE 0.013 0.001 PHE A 160 TYR 0.014 0.001 TYR A 232 ARG 0.006 0.000 ARG A 143 *********************** 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 127 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.8019 (pp30) cc_final: 0.7346 (pp30) REVERT: A 269 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: B 342 TYR cc_start: 0.7480 (p90) cc_final: 0.7112 (p90) outliers start: 10 outliers final: 7 residues processed: 124 average time/residue: 0.2309 time to fit residues: 38.3557 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 269 GLN Chi-restraints excluded: chain B residue 414 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 151 GLN ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.209772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169220 restraints weight = 9374.832| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.83 r_work: 0.3783 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8701 Z= 0.254 Angle : 0.615 7.205 11991 Z= 0.318 Chirality : 0.043 0.143 1320 Planarity : 0.005 0.051 1395 Dihedral : 15.893 81.051 1375 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.11 % Allowed : 14.99 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 955 helix: 1.35 (0.30), residues: 326 sheet: -0.82 (0.39), residues: 146 loop : -0.66 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 402 HIS 0.007 0.001 HIS A 198 PHE 0.012 0.001 PHE B 130 TYR 0.013 0.002 TYR A 232 ARG 0.007 0.001 ARG B 125 *********************** 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 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.839 Fit side-chains REVERT: A 31 ILE cc_start: 0.5221 (pt) cc_final: 0.4894 (pt) REVERT: A 145 GLN cc_start: 0.8034 (pp30) cc_final: 0.7302 (pp30) REVERT: A 269 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6974 (mp10) REVERT: A 551 LEU cc_start: 0.5360 (mp) cc_final: 0.5098 (mt) REVERT: B 198 HIS cc_start: 0.6933 (t70) cc_final: 0.6638 (t70) REVERT: B 342 TYR cc_start: 0.7558 (p90) cc_final: 0.7202 (p90) outliers start: 9 outliers final: 7 residues processed: 118 average time/residue: 0.2078 time to fit residues: 33.7817 Evaluate side-chains 115 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 31 ILE 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 73 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.210654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.170054 restraints weight = 9244.501| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.82 r_work: 0.3790 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8701 Z= 0.218 Angle : 0.587 7.247 11991 Z= 0.305 Chirality : 0.043 0.143 1320 Planarity : 0.004 0.049 1395 Dihedral : 15.772 81.198 1375 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.28), residues: 955 helix: 1.48 (0.30), residues: 324 sheet: -0.73 (0.39), residues: 144 loop : -0.64 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 402 HIS 0.005 0.001 HIS A 198 PHE 0.012 0.001 PHE A 160 TYR 0.017 0.002 TYR A 232 ARG 0.005 0.001 ARG A 143 *********************** 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 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 269 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6870 (mp10) REVERT: A 277 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6773 (mtp85) REVERT: A 530 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7366 (mtmt) REVERT: B 138 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: B 342 TYR cc_start: 0.7508 (p90) cc_final: 0.7181 (p90) outliers start: 12 outliers final: 7 residues processed: 122 average time/residue: 0.2371 time to fit residues: 38.9067 Evaluate side-chains 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 31 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL 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 36 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 0.0970 chunk 90 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 1 optimal weight: 0.0270 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 overall best weight: 1.4040 ------------------------------------------------------------------------------- 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 137 ASN A 175 ASN A 428 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.213104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172701 restraints weight = 9319.451| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.84 r_work: 0.3815 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8701 Z= 0.168 Angle : 0.568 8.945 11991 Z= 0.294 Chirality : 0.042 0.142 1320 Planarity : 0.004 0.047 1395 Dihedral : 15.590 80.934 1375 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.35 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.28), residues: 955 helix: 1.68 (0.30), residues: 326 sheet: -0.59 (0.41), residues: 138 loop : -0.55 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 402 HIS 0.003 0.001 HIS A 221 PHE 0.011 0.001 PHE A 160 TYR 0.011 0.001 TYR A 232 ARG 0.004 0.000 ARG A 143 *********************** 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 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.870 Fit side-chains REVERT: A 145 GLN cc_start: 0.8028 (pp30) cc_final: 0.7240 (pp30) REVERT: A 269 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: A 277 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6708 (mtp85) REVERT: A 358 ARG cc_start: 0.6808 (mmt90) cc_final: 0.6474 (mmm160) REVERT: B 138 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: B 198 HIS cc_start: 0.6967 (t70) cc_final: 0.6539 (t-170) REVERT: B 342 TYR cc_start: 0.7449 (p90) cc_final: 0.7179 (p90) outliers start: 11 outliers final: 8 residues processed: 124 average time/residue: 0.2346 time to fit residues: 39.8337 Evaluate side-chains 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP 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 74 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 175 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 = 0.4357 r_free = 0.4357 target = 0.205346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166035 restraints weight = 9544.786| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.90 r_work: 0.3713 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8701 Z= 0.438 Angle : 0.750 8.378 11991 Z= 0.388 Chirality : 0.048 0.162 1320 Planarity : 0.006 0.052 1395 Dihedral : 16.093 82.896 1375 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.60 % Allowed : 15.72 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.27), residues: 955 helix: 0.73 (0.29), residues: 325 sheet: -1.05 (0.40), residues: 146 loop : -0.88 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 402 HIS 0.008 0.002 HIS A 198 PHE 0.017 0.002 PHE A 160 TYR 0.021 0.003 TYR B 181 ARG 0.007 0.001 ARG B 125 *********************** 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 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 269 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 277 ARG cc_start: 0.7195 (mtp85) cc_final: 0.6862 (mtp85) REVERT: B 138 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: B 198 HIS cc_start: 0.7090 (t70) cc_final: 0.6742 (t70) REVERT: B 342 TYR cc_start: 0.7592 (p90) cc_final: 0.7297 (p90) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.2186 time to fit residues: 36.2602 Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 309 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 79 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4403 r_free = 0.4403 target = 0.210595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.169812 restraints weight = 9403.878| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.84 r_work: 0.3775 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8701 Z= 0.214 Angle : 0.615 10.327 11991 Z= 0.319 Chirality : 0.043 0.149 1320 Planarity : 0.005 0.049 1395 Dihedral : 15.887 83.949 1375 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.23 % Allowed : 17.32 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 955 helix: 1.18 (0.29), residues: 326 sheet: -0.81 (0.40), residues: 144 loop : -0.76 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 402 HIS 0.004 0.001 HIS A 198 PHE 0.014 0.001 PHE A 160 TYR 0.012 0.001 TYR B 181 ARG 0.005 0.001 ARG B 125 *********************** 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 119 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7668 (pm20) cc_final: 0.7099 (pt0) REVERT: A 102 LYS cc_start: 0.6258 (mmmt) cc_final: 0.5720 (tppt) REVERT: A 269 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6832 (mp10) REVERT: A 277 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6762 (mtp85) REVERT: A 530 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7303 (mtmt) REVERT: B 138 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: B 342 TYR cc_start: 0.7484 (p90) cc_final: 0.7260 (p90) outliers start: 10 outliers final: 8 residues processed: 119 average time/residue: 0.2245 time to fit residues: 36.5310 Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 414 TRP 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 88 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- 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 A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.208708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168174 restraints weight = 9413.341| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.83 r_work: 0.3755 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8701 Z= 0.273 Angle : 0.642 9.161 11991 Z= 0.332 Chirality : 0.043 0.147 1320 Planarity : 0.005 0.049 1395 Dihedral : 15.913 84.315 1375 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.23 % Allowed : 16.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 955 helix: 1.11 (0.29), residues: 326 sheet: -0.89 (0.40), residues: 145 loop : -0.83 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 402 HIS 0.007 0.001 HIS A 198 PHE 0.014 0.001 PHE A 160 TYR 0.014 0.002 TYR B 181 ARG 0.005 0.000 ARG B 125 ********************** 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 116 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 269 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: B 138 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: B 198 HIS cc_start: 0.7037 (t70) cc_final: 0.6664 (t-170) REVERT: B 342 TYR cc_start: 0.7485 (p90) cc_final: 0.7241 (p90) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.2195 time to fit residues: 34.8137 Evaluate side-chains 113 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL 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 5 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.211979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.171692 restraints weight = 9419.418| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.83 r_work: 0.3818 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8701 Z= 0.189 Angle : 0.596 9.738 11991 Z= 0.306 Chirality : 0.042 0.148 1320 Planarity : 0.004 0.048 1395 Dihedral : 15.649 84.610 1375 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.11 % Allowed : 16.83 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.28), residues: 955 helix: 1.47 (0.30), residues: 325 sheet: -0.72 (0.41), residues: 138 loop : -0.76 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 402 HIS 0.004 0.001 HIS A 198 PHE 0.012 0.001 PHE A 160 TYR 0.012 0.001 TYR A 318 ARG 0.004 0.000 ARG A 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3678.60 seconds wall clock time: 64 minutes 36.65 seconds (3876.65 seconds total)