Starting phenix.real_space_refine on Wed Mar 12 06:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.map" model { file = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uag_26425/03_2025/7uag_26425.cif" } resolution = 3.5 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= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4838 2.51 5 N 1318 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 7588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3794 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLU A 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU A 504 " occ=0.50 residue: pdb=" N GLU B 504 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B 504 " occ=0.50 Time building chain proxies: 5.04, per 1000 atoms: 0.66 Number of scatterers: 7588 At special positions: 0 Unit cell: (107.07, 125.33, 73.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1392 8.00 N 1318 7.00 C 4838 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 41 through 58 removed outlier: 5.272A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 3.758A pdb=" N ASP A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.958A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 454 through 465 removed outlier: 3.617A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.070A pdb=" N ASP A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 removed outlier: 5.388A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix removed outlier: 3.787A pdb=" N ASP B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.645A pdb=" N LYS B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.719A pdb=" N ARG B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.727A pdb=" N ILE B 196 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 3.639A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 removed outlier: 4.249A pdb=" N PHE B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.663A pdb=" N ASN B 302 " --> pdb=" O GLN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.529A pdb=" N THR B 319 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.835A pdb=" N ASP B 350 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 454 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 489 through 500 removed outlier: 4.117A pdb=" N ASP B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 3.828A pdb=" N VAL A 68 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR A 139 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 35 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 373 removed outlier: 3.571A pdb=" N LYS A 366 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 231 " --> pdb=" O PRO A 353 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ILE A 355 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL A 233 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE A 480 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 305 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TYR A 482 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 307 " --> pdb=" O TYR A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 393 Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.341A pdb=" N ILE B 33 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE B 35 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 356 removed outlier: 8.410A pdb=" N ILE B 355 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 233 " --> pdb=" O ILE B 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.645A pdb=" N LEU B 305 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR B 482 " --> pdb=" O LEU B 305 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 307 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 391 through 393 Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 407 285 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2296 1.33 - 1.45: 1200 1.45 - 1.57: 4203 1.57 - 1.69: 1 1.69 - 1.81: 66 Bond restraints: 7766 Sorted by residual: bond pdb=" CB PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 1.506 1.600 -0.094 3.90e-02 6.57e+02 5.76e+00 bond pdb=" C VAL A 68 " pdb=" N GLY A 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.29e+00 bond pdb=" C VAL B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.328 1.305 0.023 1.13e-02 7.83e+03 4.23e+00 bond pdb=" CA GLY B 69 " pdb=" C GLY B 69 " ideal model delta sigma weight residual 1.519 1.495 0.024 1.47e-02 4.63e+03 2.77e+00 bond pdb=" C TYR A 70 " pdb=" O TYR A 70 " ideal model delta sigma weight residual 1.235 1.215 0.021 1.26e-02 6.30e+03 2.65e+00 ... (remaining 7761 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10229 1.77 - 3.53: 227 3.53 - 5.30: 33 5.30 - 7.07: 11 7.07 - 8.84: 2 Bond angle restraints: 10502 Sorted by residual: angle pdb=" CA PRO A 172 " pdb=" N PRO A 172 " pdb=" CD PRO A 172 " ideal model delta sigma weight residual 111.50 105.35 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" N PRO A 172 " pdb=" CD PRO A 172 " pdb=" CG PRO A 172 " ideal model delta sigma weight residual 103.80 98.57 5.23 1.20e+00 6.94e-01 1.90e+01 angle pdb=" C PRO A 276 " pdb=" N ALA A 277 " pdb=" CA ALA A 277 " ideal model delta sigma weight residual 121.54 129.14 -7.60 1.91e+00 2.74e-01 1.58e+01 angle pdb=" N PRO B 172 " pdb=" CD PRO B 172 " pdb=" CG PRO B 172 " ideal model delta sigma weight residual 103.80 99.84 3.96 1.20e+00 6.94e-01 1.09e+01 angle pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" O GLY A 69 " ideal model delta sigma weight residual 122.76 119.25 3.51 1.12e+00 7.97e-01 9.81e+00 ... (remaining 10497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4262 17.98 - 35.97: 345 35.97 - 53.95: 57 53.95 - 71.93: 7 71.93 - 89.91: 3 Dihedral angle restraints: 4674 sinusoidal: 1944 harmonic: 2730 Sorted by residual: dihedral pdb=" CA MET A 207 " pdb=" C MET A 207 " pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ASN B 218 " pdb=" C ASN B 218 " pdb=" N ARG B 219 " pdb=" CA ARG B 219 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N ARG A 219 " pdb=" CA ARG A 219 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 593 0.028 - 0.056: 298 0.056 - 0.084: 144 0.084 - 0.111: 64 0.111 - 0.139: 25 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE B 196 " pdb=" N ILE B 196 " pdb=" C ILE B 196 " pdb=" CB ILE B 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA THR A 279 " pdb=" N THR A 279 " pdb=" C THR A 279 " pdb=" CB THR A 279 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 1121 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 433 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A 434 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 352 " -0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 353 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 239 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A 240 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.031 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1594 2.78 - 3.31: 7608 3.31 - 3.84: 12940 3.84 - 4.37: 14984 4.37 - 4.90: 26110 Nonbonded interactions: 63236 Sorted by model distance: nonbonded pdb=" O ILE A 80 " pdb=" OG SER A 84 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU A 274 " pdb=" ND2 ASN A 346 " model vdw 2.247 3.120 nonbonded pdb=" OE1 GLN A 209 " pdb=" NZ LYS B 407 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU B 274 " pdb=" ND2 ASN B 346 " model vdw 2.261 3.120 nonbonded pdb=" NH2 ARG B 215 " pdb=" O MET B 273 " model vdw 2.278 3.120 ... (remaining 63231 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.480 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.004 0.094 7766 Z= 0.277 Angle : 0.663 8.837 10502 Z= 0.355 Chirality : 0.045 0.139 1124 Planarity : 0.006 0.081 1374 Dihedral : 13.108 89.913 2914 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.45 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.43 (0.27), residues: 930 helix: 0.02 (0.28), residues: 330 sheet: -2.33 (0.41), residues: 142 loop : -1.13 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 225 HIS 0.004 0.001 HIS A 263 PHE 0.027 0.002 PHE A 173 TYR 0.013 0.002 TYR B 118 ARG 0.008 0.000 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.819 Fit side-chains REVERT: A 70 TYR cc_start: 0.7609 (t80) cc_final: 0.7267 (t80) REVERT: A 111 GLN cc_start: 0.6906 (mm110) cc_final: 0.6329 (mm-40) REVERT: A 137 LEU cc_start: 0.8189 (tt) cc_final: 0.7691 (tt) REVERT: B 70 TYR cc_start: 0.7377 (t80) cc_final: 0.7040 (t80) REVERT: B 111 GLN cc_start: 0.6751 (mm-40) cc_final: 0.6394 (mm-40) REVERT: B 207 MET cc_start: 0.7476 (mmm) cc_final: 0.7265 (mmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1813 time to fit residues: 28.6165 Evaluate side-chains 95 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 ASN B 201 HIS ** B 266 GLN ** 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 = 0.4686 r_free = 0.4686 target = 0.233782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.202399 restraints weight = 9631.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.206519 restraints weight = 6235.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.209407 restraints weight = 4624.677| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4477 r_free = 0.4477 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4477 r_free = 0.4477 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7766 Z= 0.186 Angle : 0.591 8.977 10502 Z= 0.306 Chirality : 0.045 0.196 1124 Planarity : 0.005 0.056 1374 Dihedral : 4.506 22.850 1032 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.24 % Allowed : 7.07 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.34 (0.27), residues: 930 helix: 0.14 (0.28), residues: 330 sheet: -2.04 (0.42), residues: 132 loop : -1.24 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 225 HIS 0.004 0.001 HIS A 201 PHE 0.018 0.002 PHE A 173 TYR 0.016 0.002 TYR B 484 ARG 0.004 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.818 Fit side-chains REVERT: A 70 TYR cc_start: 0.7320 (t80) cc_final: 0.7036 (t80) REVERT: A 95 LYS cc_start: 0.6851 (mmtt) cc_final: 0.6396 (mmtm) REVERT: A 111 GLN cc_start: 0.6781 (mm110) cc_final: 0.6199 (mm-40) REVERT: A 137 LEU cc_start: 0.8193 (tt) cc_final: 0.7681 (tt) REVERT: B 111 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6465 (mm-40) outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.1860 time to fit residues: 26.8733 Evaluate side-chains 97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN ** B 266 GLN ** 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 = 0.4685 r_free = 0.4685 target = 0.233706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.201915 restraints weight = 9798.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.206113 restraints weight = 6365.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.208762 restraints weight = 4739.215| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4466 r_free = 0.4466 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7766 Z= 0.187 Angle : 0.570 8.514 10502 Z= 0.291 Chirality : 0.044 0.173 1124 Planarity : 0.005 0.050 1374 Dihedral : 4.420 24.452 1032 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.61 % Allowed : 9.63 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.24 (0.27), residues: 930 helix: 0.18 (0.29), residues: 332 sheet: -1.96 (0.41), residues: 138 loop : -1.14 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 164 HIS 0.004 0.001 HIS A 201 PHE 0.022 0.002 PHE A 253 TYR 0.024 0.002 TYR B 70 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.788 Fit side-chains REVERT: A 95 LYS cc_start: 0.6947 (mmtt) cc_final: 0.6509 (mmtm) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1847 time to fit residues: 26.1189 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 81 optimal weight: 0.0270 chunk 50 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 266 GLN ** 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 = 0.4705 r_free = 0.4705 target = 0.235961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.204468 restraints weight = 9644.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.208540 restraints weight = 6281.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.211309 restraints weight = 4666.642| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7766 Z= 0.165 Angle : 0.557 8.468 10502 Z= 0.282 Chirality : 0.043 0.187 1124 Planarity : 0.004 0.049 1374 Dihedral : 4.323 26.462 1032 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.61 % Allowed : 11.59 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.05 (0.27), residues: 930 helix: 0.32 (0.29), residues: 332 sheet: -1.64 (0.39), residues: 154 loop : -1.04 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 164 HIS 0.003 0.001 HIS A 201 PHE 0.024 0.001 PHE B 253 TYR 0.023 0.001 TYR B 70 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.796 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.1807 time to fit residues: 25.2237 Evaluate side-chains 91 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 266 GLN ** 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 = 0.4839 r_free = 0.4839 target = 0.253889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.225318 restraints weight = 9801.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.226710 restraints weight = 6948.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.229874 restraints weight = 5414.458| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4628 r_free = 0.4628 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4627 r_free = 0.4627 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7766 Z= 0.175 Angle : 0.561 8.491 10502 Z= 0.283 Chirality : 0.043 0.183 1124 Planarity : 0.004 0.047 1374 Dihedral : 4.284 27.773 1032 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.10 % Allowed : 13.29 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.07 (0.27), residues: 930 helix: 0.34 (0.29), residues: 332 sheet: -1.86 (0.41), residues: 138 loop : -1.05 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 164 HIS 0.002 0.001 HIS A 201 PHE 0.020 0.001 PHE A 253 TYR 0.023 0.002 TYR B 70 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.774 Fit side-chains REVERT: B 465 PHE cc_start: 0.6346 (t80) cc_final: 0.6109 (t80) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.1766 time to fit residues: 25.0962 Evaluate side-chains 98 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.247735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.218820 restraints weight = 9873.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.218935 restraints weight = 7161.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.220529 restraints weight = 6259.228| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4548 r_free = 0.4548 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4548 r_free = 0.4548 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7766 Z= 0.315 Angle : 0.637 9.197 10502 Z= 0.324 Chirality : 0.045 0.210 1124 Planarity : 0.005 0.047 1374 Dihedral : 4.624 29.658 1032 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.95 % Allowed : 13.78 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.33 (0.27), residues: 930 helix: -0.02 (0.28), residues: 336 sheet: -2.21 (0.40), residues: 146 loop : -0.96 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 349 HIS 0.003 0.001 HIS A 201 PHE 0.023 0.002 PHE A 173 TYR 0.025 0.002 TYR B 484 ARG 0.009 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.855 Fit side-chains REVERT: B 322 TYR cc_start: 0.7724 (t80) cc_final: 0.7418 (t80) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.1759 time to fit residues: 27.3620 Evaluate side-chains 105 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN ** B 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.251691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.220650 restraints weight = 9785.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.224606 restraints weight = 6537.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.226897 restraints weight = 4988.035| |-----------------------------------------------------------------------------| r_work (final): 0.4600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7766 Z= 0.191 Angle : 0.595 9.343 10502 Z= 0.300 Chirality : 0.044 0.160 1124 Planarity : 0.004 0.052 1374 Dihedral : 4.435 27.486 1032 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.34 % Allowed : 15.49 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.21 (0.27), residues: 930 helix: 0.11 (0.29), residues: 336 sheet: -1.99 (0.42), residues: 138 loop : -1.02 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 225 HIS 0.002 0.001 HIS A 201 PHE 0.024 0.002 PHE A 102 TYR 0.022 0.002 TYR B 70 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.792 Fit side-chains REVERT: A 137 LEU cc_start: 0.8304 (tt) cc_final: 0.8060 (tt) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.1817 time to fit residues: 25.0818 Evaluate side-chains 101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 31 optimal weight: 0.0970 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** 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 = 0.4832 r_free = 0.4832 target = 0.252780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225868 restraints weight = 9910.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.226079 restraints weight = 7597.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.227676 restraints weight = 7367.420| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7766 Z= 0.179 Angle : 0.581 9.477 10502 Z= 0.290 Chirality : 0.043 0.148 1124 Planarity : 0.004 0.050 1374 Dihedral : 4.297 26.488 1032 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.59 % Allowed : 15.37 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.11 (0.27), residues: 930 helix: 0.20 (0.29), residues: 336 sheet: -1.93 (0.41), residues: 138 loop : -0.97 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 164 HIS 0.002 0.001 HIS A 155 PHE 0.019 0.002 PHE A 102 TYR 0.016 0.001 TYR B 484 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.8299 (tt) cc_final: 0.8034 (tt) REVERT: B 465 PHE cc_start: 0.6362 (t80) cc_final: 0.5956 (t80) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.1776 time to fit residues: 25.0346 Evaluate side-chains 97 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 0.0170 overall best weight: 2.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** 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 = 0.4803 r_free = 0.4803 target = 0.248833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.219537 restraints weight = 9900.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.220696 restraints weight = 7342.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.222543 restraints weight = 5687.995| |-----------------------------------------------------------------------------| r_work (final): 0.4567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4567 r_free = 0.4567 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4567 r_free = 0.4567 target_work(ls_wunit_k1) = 0.218 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7766 Z= 0.270 Angle : 0.631 10.182 10502 Z= 0.318 Chirality : 0.045 0.161 1124 Planarity : 0.005 0.049 1374 Dihedral : 4.480 26.715 1032 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.22 % Allowed : 15.73 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.28 (0.27), residues: 930 helix: -0.00 (0.28), residues: 336 sheet: -2.32 (0.41), residues: 140 loop : -0.89 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 349 HIS 0.002 0.001 HIS B 186 PHE 0.021 0.002 PHE A 173 TYR 0.023 0.002 TYR B 484 ARG 0.007 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.783 Fit side-chains REVERT: A 495 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.3821 (tp) REVERT: B 322 TYR cc_start: 0.7798 (t80) cc_final: 0.7446 (t80) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.1785 time to fit residues: 27.0948 Evaluate side-chains 106 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 1.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN ** B 266 GLN ** 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 = 0.4818 r_free = 0.4818 target = 0.250836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.224380 restraints weight = 9850.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.223749 restraints weight = 7373.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.224764 restraints weight = 6477.081| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4588 r_free = 0.4588 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4588 r_free = 0.4588 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7766 Z= 0.214 Angle : 0.621 9.167 10502 Z= 0.311 Chirality : 0.044 0.170 1124 Planarity : 0.004 0.054 1374 Dihedral : 4.448 26.299 1032 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.98 % Allowed : 17.07 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.27 (0.27), residues: 930 helix: -0.02 (0.28), residues: 336 sheet: -2.08 (0.41), residues: 138 loop : -0.96 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 164 HIS 0.002 0.001 HIS A 263 PHE 0.020 0.002 PHE B 173 TYR 0.019 0.002 TYR B 484 ARG 0.006 0.000 ARG A 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.799 Fit side-chains REVERT: A 495 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4145 (tp) REVERT: B 322 TYR cc_start: 0.7760 (t80) cc_final: 0.7478 (t80) outliers start: 8 outliers final: 7 residues processed: 98 average time/residue: 0.1825 time to fit residues: 25.3811 Evaluate side-chains 96 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 405 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.255206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.230286 restraints weight = 9788.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.229315 restraints weight = 7371.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.230244 restraints weight = 6659.872| |-----------------------------------------------------------------------------| r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4635 r_free = 0.4635 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4635 r_free = 0.4635 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7766 Z= 0.165 Angle : 0.593 9.319 10502 Z= 0.294 Chirality : 0.043 0.145 1124 Planarity : 0.004 0.057 1374 Dihedral : 4.250 25.715 1032 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.73 % Allowed : 17.20 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.10 (0.27), residues: 930 helix: 0.16 (0.28), residues: 336 sheet: -1.75 (0.40), residues: 150 loop : -0.95 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 164 HIS 0.002 0.001 HIS A 263 PHE 0.019 0.001 PHE A 102 TYR 0.024 0.002 TYR B 70 ARG 0.006 0.000 ARG A 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2447.60 seconds wall clock time: 43 minutes 18.17 seconds (2598.17 seconds total)