Starting phenix.real_space_refine on Wed Sep 17 12:00:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb8_43116/09_2025/8vb8_43116.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 13 5.16 5 C 5380 2.51 5 N 1416 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8511 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4480 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 553, 4473 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 515} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4582 Chain: "B" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3238 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 761 Classifications: {'DNA': 35, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 36} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 2, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.76, per 1000 atoms: 0.32 Number of scatterers: 8511 At special positions: 0 Unit cell: (79.2, 96.525, 124.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 13 16.00 P 40 15.00 Mg 2 11.99 O 1660 8.00 N 1416 7.00 C 5380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 469.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.8% alpha, 14.1% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 3.699A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.585A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.615A pdb=" N HIS A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 removed outlier: 3.512A pdb=" N GLN A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.647A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 363 through 384 removed outlier: 3.640A pdb=" N VAL A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.130A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.637A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 77 through 85 removed outlier: 4.058A pdb=" N GLN B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.507A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 160 removed outlier: 4.037A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 168 removed outlier: 6.029A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 194 through 213 removed outlier: 3.629A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.836A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.123A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.612A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 406 removed outlier: 3.530A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) 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 60 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 4.175A pdb=" N TRP A 252 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 354 removed outlier: 8.611A pdb=" N ASN A 348 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN A 343 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 443 through 446 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 64 Processing sheet with id=AB3, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.861A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 331 removed outlier: 7.204A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 391 removed outlier: 6.218A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 288 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 1.06 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: 2152 1.33 - 1.45: 1739 1.45 - 1.57: 4818 1.57 - 1.69: 79 1.69 - 1.80: 23 Bond restraints: 8811 Sorted by residual: bond pdb=" C1' DTP A 701 " pdb=" N9 DTP A 701 " ideal model delta sigma weight residual 1.457 1.408 0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" O2B DTP A 701 " pdb=" PB DTP A 701 " ideal model delta sigma weight residual 1.529 1.460 0.069 2.20e-02 2.07e+03 9.98e+00 bond pdb=" N ILE B 94 " pdb=" CA ILE B 94 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.23e-02 6.61e+03 9.48e+00 bond pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.30e+00 bond pdb=" CA SER A 134 " pdb=" CB SER A 134 " ideal model delta sigma weight residual 1.535 1.490 0.045 1.51e-02 4.39e+03 8.75e+00 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11814 1.71 - 3.43: 266 3.43 - 5.14: 52 5.14 - 6.86: 14 6.86 - 8.57: 5 Bond angle restraints: 12151 Sorted by residual: angle pdb=" PB DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sigma weight residual 139.87 134.07 5.80 1.00e+00 1.00e+00 3.36e+01 angle pdb=" CA GLU A 297 " pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 114.10 122.45 -8.35 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CA THR A 107 " pdb=" C THR A 107 " pdb=" O THR A 107 " ideal model delta sigma weight residual 120.60 116.06 4.54 1.20e+00 6.94e-01 1.43e+01 angle pdb=" CB ARG B 277 " pdb=" CG ARG B 277 " pdb=" CD ARG B 277 " ideal model delta sigma weight residual 111.30 119.87 -8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CA VAL A 108 " pdb=" C VAL A 108 " pdb=" O VAL A 108 " ideal model delta sigma weight residual 120.48 116.80 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 12146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.61: 4683 30.61 - 61.22: 462 61.22 - 91.83: 30 91.83 - 122.44: 0 122.44 - 153.06: 1 Dihedral angle restraints: 5176 sinusoidal: 2393 harmonic: 2783 Sorted by residual: dihedral pdb=" CA PRO A 420 " pdb=" C PRO A 420 " pdb=" N PRO A 421 " pdb=" CA PRO A 421 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O1B DTP A 701 " pdb=" O3B DTP A 701 " pdb=" PB DTP A 701 " pdb=" PG DTP A 701 " ideal model delta sinusoidal sigma weight residual 299.93 146.87 153.06 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C ILE B 94 " pdb=" N ILE B 94 " pdb=" CA ILE B 94 " pdb=" CB ILE B 94 " ideal model delta harmonic sigma weight residual -122.00 -131.06 9.06 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 5173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1291 0.103 - 0.207: 41 0.207 - 0.310: 1 0.310 - 0.414: 0 0.414 - 0.517: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" P DT F 17 " pdb=" OP1 DT F 17 " pdb=" OP2 DT F 17 " pdb=" O5' DT F 17 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB ILE B 94 " pdb=" CA ILE B 94 " pdb=" CG1 ILE B 94 " pdb=" CG2 ILE B 94 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1331 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 419 " -0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 420 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 421 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 414 " -0.018 2.00e-02 2.50e+03 1.52e-02 5.74e+00 pdb=" CG TRP A 414 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 414 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 414 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 414 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 414 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 414 " -0.003 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 91 2.60 - 3.17: 6694 3.17 - 3.75: 13546 3.75 - 4.32: 18910 4.32 - 4.90: 30801 Nonbonded interactions: 70042 Sorted by model distance: nonbonded pdb=" OD1 ASP A 110 " pdb="MG MG A 702 " model vdw 2.019 2.170 nonbonded pdb=" O VAL A 111 " pdb="MG MG A 702 " model vdw 2.119 2.170 nonbonded pdb=" O THR A 439 " pdb=" OG1 THR A 459 " model vdw 2.241 3.040 nonbonded pdb=" O VAL B 372 " pdb=" OG1 THR B 376 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 280 " pdb=" O3' DC F 7 " model vdw 2.254 3.040 ... (remaining 70037 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=0.50 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: 4.360 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 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 0.086 8811 Z= 0.216 Angle : 0.663 8.573 12151 Z= 0.374 Chirality : 0.045 0.517 1334 Planarity : 0.006 0.096 1399 Dihedral : 21.076 153.056 3380 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 4.88 % Allowed : 32.02 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.28), residues: 944 helix: 0.26 (0.31), residues: 317 sheet: -0.95 (0.38), residues: 188 loop : -1.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 277 TYR 0.020 0.001 TYR B 354 PHE 0.010 0.001 PHE B 87 TRP 0.041 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8811) covalent geometry : angle 0.66274 (12151) hydrogen bonds : bond 0.19058 ( 324) hydrogen bonds : angle 6.67212 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 0.303 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 0.4906 time to fit residues: 53.7710 Evaluate side-chains 97 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 61 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 422 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 0.0170 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** B 161 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 = 0.3705 r_free = 0.3705 target = 0.116507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.080126 restraints weight = 20181.015| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.12 r_work: 0.2942 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8811 Z= 0.130 Angle : 0.551 8.157 12151 Z= 0.289 Chirality : 0.041 0.161 1334 Planarity : 0.005 0.089 1399 Dihedral : 16.852 158.132 1472 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 4.17 % Allowed : 30.83 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.28), residues: 944 helix: 0.83 (0.31), residues: 316 sheet: -0.93 (0.37), residues: 193 loop : -1.22 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 358 TYR 0.030 0.001 TYR A 457 PHE 0.012 0.001 PHE B 87 TRP 0.022 0.001 TRP A 414 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8811) covalent geometry : angle 0.55095 (12151) hydrogen bonds : bond 0.03452 ( 324) hydrogen bonds : angle 4.54113 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.313 Fit side-chains REVERT: A 358 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7909 (mtp85) REVERT: A 480 GLN cc_start: 0.8506 (tp40) cc_final: 0.8214 (mm-40) REVERT: A 535 TRP cc_start: 0.8243 (t60) cc_final: 0.7615 (t60) REVERT: B 186 ASP cc_start: 0.7250 (m-30) cc_final: 0.7044 (m-30) REVERT: B 353 LYS cc_start: 0.9050 (tttp) cc_final: 0.8441 (ttpp) REVERT: B 395 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8510 (tttm) outliers start: 35 outliers final: 19 residues processed: 105 average time/residue: 0.4803 time to fit residues: 54.3398 Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.113132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077041 restraints weight = 15200.719| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.70 r_work: 0.2892 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 8811 Z= 0.285 Angle : 0.613 6.970 12151 Z= 0.320 Chirality : 0.044 0.168 1334 Planarity : 0.005 0.083 1399 Dihedral : 16.882 147.787 1437 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.53 % Rotamer: Outliers : 3.93 % Allowed : 30.60 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.28), residues: 944 helix: 0.72 (0.31), residues: 324 sheet: -0.77 (0.39), residues: 177 loop : -1.22 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 83 TYR 0.030 0.001 TYR A 457 PHE 0.013 0.002 PHE A 160 TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00682 ( 8811) covalent geometry : angle 0.61344 (12151) hydrogen bonds : bond 0.03966 ( 324) hydrogen bonds : angle 4.45679 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8415 (p0) REVERT: A 373 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: A 484 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9158 (tp) REVERT: A 530 LYS cc_start: 0.8190 (mttp) cc_final: 0.7966 (mmmm) REVERT: A 535 TRP cc_start: 0.8508 (t60) cc_final: 0.7877 (t60) REVERT: B 186 ASP cc_start: 0.7420 (m-30) cc_final: 0.7203 (m-30) REVERT: B 270 ILE cc_start: 0.8653 (tt) cc_final: 0.8208 (pt) REVERT: B 353 LYS cc_start: 0.9154 (tttp) cc_final: 0.8552 (ttpp) outliers start: 33 outliers final: 19 residues processed: 90 average time/residue: 0.5478 time to fit residues: 53.0252 Evaluate side-chains 80 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 336 GLN B 418 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077517 restraints weight = 18313.037| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.13 r_work: 0.2912 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8811 Z= 0.152 Angle : 0.550 6.999 12151 Z= 0.287 Chirality : 0.041 0.157 1334 Planarity : 0.005 0.076 1399 Dihedral : 16.465 140.062 1434 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.59 % Rotamer: Outliers : 3.45 % Allowed : 31.07 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.28), residues: 944 helix: 1.03 (0.31), residues: 317 sheet: -0.71 (0.40), residues: 166 loop : -1.12 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.033 0.001 TYR A 457 PHE 0.011 0.001 PHE B 87 TRP 0.014 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8811) covalent geometry : angle 0.54999 (12151) hydrogen bonds : bond 0.03178 ( 324) hydrogen bonds : angle 4.15400 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 530 LYS cc_start: 0.7992 (mttp) cc_final: 0.7789 (mmmm) REVERT: A 535 TRP cc_start: 0.8378 (t60) cc_final: 0.7840 (t60) REVERT: B 270 ILE cc_start: 0.8724 (tt) cc_final: 0.8331 (pt) REVERT: B 336 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: B 353 LYS cc_start: 0.9023 (tttp) cc_final: 0.8477 (ttmm) outliers start: 29 outliers final: 15 residues processed: 92 average time/residue: 0.5159 time to fit residues: 51.0459 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.114279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.076770 restraints weight = 24871.575| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.44 r_work: 0.2871 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8811 Z= 0.193 Angle : 0.567 8.059 12151 Z= 0.294 Chirality : 0.042 0.158 1334 Planarity : 0.005 0.067 1399 Dihedral : 16.336 139.681 1426 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.94 % Favored : 93.85 % Rotamer: Outliers : 3.57 % Allowed : 31.19 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.28), residues: 944 helix: 1.08 (0.31), residues: 315 sheet: -0.71 (0.39), residues: 172 loop : -1.12 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.017 0.001 TYR B 354 PHE 0.011 0.001 PHE A 160 TRP 0.033 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8811) covalent geometry : angle 0.56702 (12151) hydrogen bonds : bond 0.03270 ( 324) hydrogen bonds : angle 4.15174 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 530 LYS cc_start: 0.8035 (mttp) cc_final: 0.7830 (mmmm) REVERT: A 535 TRP cc_start: 0.8494 (t60) cc_final: 0.8002 (t60) REVERT: B 270 ILE cc_start: 0.8719 (tt) cc_final: 0.8357 (pt) REVERT: B 353 LYS cc_start: 0.9065 (tttp) cc_final: 0.8516 (ttmm) outliers start: 30 outliers final: 19 residues processed: 89 average time/residue: 0.5572 time to fit residues: 53.4071 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 38 optimal weight: 0.0170 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 32 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078885 restraints weight = 18255.351| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.07 r_work: 0.2909 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8811 Z= 0.116 Angle : 0.534 7.635 12151 Z= 0.275 Chirality : 0.040 0.137 1334 Planarity : 0.004 0.054 1399 Dihedral : 16.059 131.229 1426 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 3.10 % Allowed : 31.43 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.28), residues: 944 helix: 1.43 (0.32), residues: 307 sheet: -0.67 (0.39), residues: 175 loop : -1.03 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 83 TYR 0.033 0.001 TYR A 457 PHE 0.017 0.001 PHE B 87 TRP 0.024 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8811) covalent geometry : angle 0.53434 (12151) hydrogen bonds : bond 0.02800 ( 324) hydrogen bonds : angle 3.95709 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6979 (mp10) REVERT: A 535 TRP cc_start: 0.8401 (t60) cc_final: 0.7872 (t60) REVERT: A 536 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8165 (m) REVERT: B 193 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8547 (pp) REVERT: B 270 ILE cc_start: 0.8729 (tt) cc_final: 0.8429 (pt) REVERT: B 353 LYS cc_start: 0.9005 (tttp) cc_final: 0.8439 (ttmm) REVERT: B 354 TYR cc_start: 0.7631 (t80) cc_final: 0.7394 (t80) outliers start: 26 outliers final: 15 residues processed: 90 average time/residue: 0.5084 time to fit residues: 49.2156 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TRP Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.078638 restraints weight = 17990.922| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.97 r_work: 0.2914 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8811 Z= 0.135 Angle : 0.539 7.385 12151 Z= 0.276 Chirality : 0.041 0.146 1334 Planarity : 0.004 0.054 1399 Dihedral : 15.990 127.956 1426 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 3.45 % Allowed : 31.19 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.28), residues: 944 helix: 1.53 (0.32), residues: 307 sheet: -0.70 (0.38), residues: 183 loop : -0.96 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.031 0.001 TYR A 457 PHE 0.009 0.001 PHE A 160 TRP 0.030 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8811) covalent geometry : angle 0.53862 (12151) hydrogen bonds : bond 0.02883 ( 324) hydrogen bonds : angle 3.92939 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 308 GLU cc_start: 0.9032 (tp30) cc_final: 0.8821 (tp30) REVERT: A 358 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8160 (mtp85) REVERT: A 373 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: A 535 TRP cc_start: 0.8462 (t60) cc_final: 0.7917 (t60) REVERT: A 536 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 192 ASP cc_start: 0.8834 (t0) cc_final: 0.8429 (m-30) REVERT: B 193 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8875 (pp) REVERT: B 270 ILE cc_start: 0.8828 (tt) cc_final: 0.8530 (pt) REVERT: B 353 LYS cc_start: 0.9012 (tttp) cc_final: 0.8442 (ttmm) REVERT: B 354 TYR cc_start: 0.7636 (t80) cc_final: 0.7378 (t80) REVERT: B 356 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7685 (ptp90) outliers start: 29 outliers final: 15 residues processed: 87 average time/residue: 0.5230 time to fit residues: 49.1224 Evaluate side-chains 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079078 restraints weight = 17879.620| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.93 r_work: 0.2889 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8811 Z= 0.174 Angle : 0.551 8.026 12151 Z= 0.283 Chirality : 0.041 0.153 1334 Planarity : 0.004 0.059 1399 Dihedral : 15.965 129.806 1424 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 2.50 % Allowed : 31.90 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.28), residues: 944 helix: 1.55 (0.32), residues: 307 sheet: -0.67 (0.39), residues: 179 loop : -0.90 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.033 0.001 TYR A 457 PHE 0.019 0.001 PHE B 87 TRP 0.027 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8811) covalent geometry : angle 0.55061 (12151) hydrogen bonds : bond 0.03048 ( 324) hydrogen bonds : angle 3.97169 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6971 (mp10) REVERT: A 535 TRP cc_start: 0.8473 (t60) cc_final: 0.7922 (t60) REVERT: A 536 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 192 ASP cc_start: 0.8829 (t0) cc_final: 0.8464 (m-30) REVERT: B 193 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8838 (pp) REVERT: B 270 ILE cc_start: 0.8794 (tt) cc_final: 0.8502 (pt) REVERT: B 353 LYS cc_start: 0.9006 (tttp) cc_final: 0.8436 (ttmm) REVERT: B 354 TYR cc_start: 0.7675 (t80) cc_final: 0.7386 (t80) REVERT: B 356 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7712 (ptp90) outliers start: 21 outliers final: 13 residues processed: 75 average time/residue: 0.5703 time to fit residues: 45.9270 Evaluate side-chains 74 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.116801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.080848 restraints weight = 18189.551| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.94 r_work: 0.2922 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.123 Angle : 0.537 8.571 12151 Z= 0.274 Chirality : 0.040 0.147 1334 Planarity : 0.004 0.065 1399 Dihedral : 15.726 121.984 1423 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 2.26 % Allowed : 32.02 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.28), residues: 944 helix: 1.67 (0.32), residues: 307 sheet: -0.63 (0.37), residues: 188 loop : -0.89 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 83 TYR 0.034 0.001 TYR A 457 PHE 0.008 0.001 PHE A 160 TRP 0.025 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8811) covalent geometry : angle 0.53674 (12151) hydrogen bonds : bond 0.02687 ( 324) hydrogen bonds : angle 3.86470 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8121 (mtp85) REVERT: A 373 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6936 (mp10) REVERT: A 535 TRP cc_start: 0.8465 (t60) cc_final: 0.7885 (t60) REVERT: B 192 ASP cc_start: 0.8767 (t0) cc_final: 0.8449 (m-30) REVERT: B 193 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 270 ILE cc_start: 0.8808 (tt) cc_final: 0.8552 (pt) REVERT: B 353 LYS cc_start: 0.8997 (tttp) cc_final: 0.8429 (ttmm) REVERT: B 354 TYR cc_start: 0.7646 (t80) cc_final: 0.7379 (t80) REVERT: B 356 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7693 (ptp90) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.5999 time to fit residues: 48.2082 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.116747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079775 restraints weight = 24964.210| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.45 r_work: 0.2883 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8811 Z= 0.187 Angle : 0.884 59.197 12151 Z= 0.507 Chirality : 0.042 0.332 1334 Planarity : 0.005 0.065 1399 Dihedral : 15.722 122.036 1421 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 2.26 % Allowed : 32.38 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.28), residues: 944 helix: 1.66 (0.32), residues: 307 sheet: -0.62 (0.37), residues: 188 loop : -0.90 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.032 0.001 TYR A 457 PHE 0.011 0.001 PHE B 87 TRP 0.023 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8811) covalent geometry : angle 0.88416 (12151) hydrogen bonds : bond 0.02707 ( 324) hydrogen bonds : angle 3.86492 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8132 (mtp85) REVERT: A 373 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6983 (mp10) REVERT: A 535 TRP cc_start: 0.8460 (t60) cc_final: 0.7878 (t60) REVERT: B 192 ASP cc_start: 0.8767 (t0) cc_final: 0.8430 (m-30) REVERT: B 193 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8778 (pp) REVERT: B 270 ILE cc_start: 0.8731 (tt) cc_final: 0.8465 (pt) REVERT: B 353 LYS cc_start: 0.9010 (tttp) cc_final: 0.8435 (ttmm) REVERT: B 356 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7692 (ptp90) outliers start: 19 outliers final: 12 residues processed: 72 average time/residue: 0.6096 time to fit residues: 46.9852 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 340 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 = 0.3685 r_free = 0.3685 target = 0.116180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079941 restraints weight = 17852.204| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.94 r_work: 0.2927 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 8811 Z= 0.186 Angle : 0.884 59.175 12151 Z= 0.507 Chirality : 0.042 0.331 1334 Planarity : 0.005 0.065 1399 Dihedral : 15.722 122.036 1421 Min Nonbonded Distance : 1.009 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 1.90 % Allowed : 32.86 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.28), residues: 944 helix: 1.66 (0.32), residues: 307 sheet: -0.62 (0.37), residues: 188 loop : -0.90 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.032 0.001 TYR A 457 PHE 0.011 0.001 PHE B 87 TRP 0.023 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8811) covalent geometry : angle 0.88401 (12151) hydrogen bonds : bond 0.02707 ( 324) hydrogen bonds : angle 3.86492 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2906.48 seconds wall clock time: 50 minutes 23.13 seconds (3023.13 seconds total)