Starting phenix.real_space_refine on Wed Jan 15 15:38:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vb8_43116/01_2025/8vb8_43116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vb8_43116/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vb8_43116/01_2025/8vb8_43116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vb8_43116/01_2025/8vb8_43116.map" model { file = "/net/cci-nas-00/data/ceres_data/8vb8_43116/01_2025/8vb8_43116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vb8_43116/01_2025/8vb8_43116.cif" } resolution = 3.0 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP: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: 8.01, per 1000 atoms: 0.94 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: 2.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 2.38 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: 2.55 Time building geometry restraints manager: 2.59 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.850 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.580 ------------------------------------------------------------------------------- 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= 0.255 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 (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 (0.28), 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 TRP 0.041 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.010 0.001 PHE B 87 TYR 0.020 0.001 TYR B 354 ARG 0.011 0.001 ARG B 277 *********************** 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 : 0.907 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 102 average time/residue: 1.0707 time to fit residues: 117.9647 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 : 0.890 ------------------------------------------------------------------------------- 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 81 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.114011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.077644 restraints weight = 17806.107| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.93 r_work: 0.2903 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 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 : 0.005 0.082 8811 Z= 0.329 Angle : 0.589 8.065 12151 Z= 0.308 Chirality : 0.043 0.165 1334 Planarity : 0.005 0.090 1399 Dihedral : 17.069 152.822 1472 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.15 % Favored : 93.64 % Rotamer: Outliers : 3.81 % Allowed : 31.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.28), residues: 944 helix: 0.61 (0.31), residues: 323 sheet: -0.92 (0.38), residues: 188 loop : -1.30 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.012 0.001 PHE B 61 TYR 0.029 0.001 TYR A 457 ARG 0.007 0.001 ARG A 358 *********************** 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 95 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 63 time to evaluate : 0.895 Fit side-chains REVERT: A 358 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8055 (mtp85) REVERT: A 530 LYS cc_start: 0.8137 (mttp) cc_final: 0.7912 (mmmm) REVERT: A 535 TRP cc_start: 0.8313 (t60) cc_final: 0.7687 (t60) REVERT: B 186 ASP cc_start: 0.7304 (m-30) cc_final: 0.7075 (m-30) REVERT: B 353 LYS cc_start: 0.9055 (tttp) cc_final: 0.8441 (ttpp) outliers start: 32 outliers final: 19 residues processed: 94 average time/residue: 1.0176 time to fit residues: 104.0345 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 362 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 515 SER 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 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 447 ASN ** 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 = 0.3703 r_free = 0.3703 target = 0.117169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078925 restraints weight = 18116.637| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.15 r_work: 0.2930 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8811 Z= 0.206 Angle : 0.542 7.088 12151 Z= 0.283 Chirality : 0.041 0.161 1334 Planarity : 0.005 0.083 1399 Dihedral : 16.599 143.015 1438 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.77 % Favored : 95.02 % Rotamer: Outliers : 4.29 % Allowed : 30.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.28), residues: 944 helix: 1.00 (0.31), residues: 318 sheet: -0.88 (0.37), residues: 192 loop : -1.18 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.008 0.001 PHE A 160 TYR 0.030 0.001 TYR A 457 ARG 0.009 0.001 ARG B 83 *********************** 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 104 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8057 (mtp85) REVERT: A 480 GLN cc_start: 0.8549 (tp40) cc_final: 0.8278 (mm-40) REVERT: A 535 TRP cc_start: 0.8323 (t60) cc_final: 0.7866 (t60) REVERT: B 270 ILE cc_start: 0.8643 (tt) cc_final: 0.8209 (pt) REVERT: B 353 LYS cc_start: 0.9036 (tttp) cc_final: 0.8405 (ttpp) outliers start: 36 outliers final: 20 residues processed: 102 average time/residue: 1.0659 time to fit residues: 117.8379 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 179 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 280 SER 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 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 417 VAL Chi-restraints excluded: chain B residue 418 ASN 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 66 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.116153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080340 restraints weight = 17805.976| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.91 r_work: 0.2942 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8811 Z= 0.201 Angle : 0.540 7.040 12151 Z= 0.281 Chirality : 0.041 0.158 1334 Planarity : 0.005 0.074 1399 Dihedral : 16.332 136.292 1431 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.09 % Favored : 94.70 % Rotamer: Outliers : 3.57 % Allowed : 30.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.28), residues: 944 helix: 1.14 (0.31), residues: 317 sheet: -0.81 (0.37), residues: 192 loop : -1.17 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 414 HIS 0.003 0.001 HIS A 221 PHE 0.013 0.001 PHE B 87 TYR 0.033 0.001 TYR A 457 ARG 0.008 0.000 ARG B 83 *********************** 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 90 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8166 (mtp85) REVERT: A 373 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: A 535 TRP cc_start: 0.8390 (t60) cc_final: 0.7842 (t60) REVERT: B 193 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 353 LYS cc_start: 0.9011 (tttp) cc_final: 0.8401 (ttpp) REVERT: B 354 TYR cc_start: 0.7751 (t80) cc_final: 0.7527 (t80) outliers start: 30 outliers final: 16 residues processed: 88 average time/residue: 1.1217 time to fit residues: 106.2304 Evaluate side-chains 73 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 280 SER 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 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 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 269 GLN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076450 restraints weight = 24585.176| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.53 r_work: 0.2849 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8811 Z= 0.250 Angle : 0.543 7.030 12151 Z= 0.283 Chirality : 0.041 0.158 1334 Planarity : 0.005 0.065 1399 Dihedral : 16.298 133.992 1430 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.83 % Favored : 93.96 % Rotamer: Outliers : 3.33 % Allowed : 30.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 944 helix: 1.33 (0.32), residues: 310 sheet: -0.75 (0.37), residues: 192 loop : -1.11 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE A 61 TYR 0.031 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** 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 89 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 373 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: A 535 TRP cc_start: 0.8435 (t60) cc_final: 0.7915 (t60) REVERT: B 193 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8522 (pp) REVERT: B 270 ILE cc_start: 0.8670 (tt) cc_final: 0.8343 (pt) REVERT: B 353 LYS cc_start: 0.9042 (tttp) cc_final: 0.8495 (ttmm) REVERT: B 354 TYR cc_start: 0.7741 (t80) cc_final: 0.7460 (t80) REVERT: B 356 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7788 (ptp90) outliers start: 28 outliers final: 16 residues processed: 86 average time/residue: 1.1076 time to fit residues: 102.7209 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 : 0.907 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 497 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 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 = 0.3658 r_free = 0.3658 target = 0.115482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.077093 restraints weight = 24601.057| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.54 r_work: 0.2855 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8811 Z= 0.225 Angle : 0.543 7.315 12151 Z= 0.281 Chirality : 0.041 0.148 1334 Planarity : 0.004 0.053 1399 Dihedral : 16.184 131.523 1429 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 3.57 % Allowed : 30.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 944 helix: 1.45 (0.32), residues: 307 sheet: -0.79 (0.37), residues: 194 loop : -1.00 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.016 0.001 PHE B 87 TYR 0.037 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** 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 89 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8190 (mtp85) REVERT: A 373 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: A 535 TRP cc_start: 0.8433 (t60) cc_final: 0.7880 (t60) REVERT: B 193 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8908 (pp) REVERT: B 270 ILE cc_start: 0.8665 (tt) cc_final: 0.8383 (pt) REVERT: B 336 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: B 353 LYS cc_start: 0.9051 (tttp) cc_final: 0.8483 (ttmm) REVERT: B 354 TYR cc_start: 0.7732 (t80) cc_final: 0.7508 (t80) REVERT: B 356 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7772 (ptp90) outliers start: 30 outliers final: 15 residues processed: 86 average time/residue: 1.0890 time to fit residues: 101.0860 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 280 SER 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 497 THR 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 336 GLN Chi-restraints excluded: chain B residue 356 ARG 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 49 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 460 ASN ** 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 = 0.3679 r_free = 0.3679 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079176 restraints weight = 14491.259| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.72 r_work: 0.2931 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8811 Z= 0.199 Angle : 0.534 7.767 12151 Z= 0.275 Chirality : 0.041 0.139 1334 Planarity : 0.004 0.054 1399 Dihedral : 16.065 128.238 1428 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 3.69 % Allowed : 30.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 944 helix: 1.56 (0.32), residues: 307 sheet: -0.75 (0.38), residues: 188 loop : -0.98 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE B 87 TYR 0.030 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** 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 92 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 358 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8179 (mtp85) REVERT: A 373 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: A 535 TRP cc_start: 0.8468 (t60) cc_final: 0.7927 (t60) REVERT: B 193 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8845 (pp) REVERT: B 270 ILE cc_start: 0.8815 (tt) cc_final: 0.8536 (pt) REVERT: B 353 LYS cc_start: 0.9008 (tttp) cc_final: 0.8429 (ttmm) REVERT: B 354 TYR cc_start: 0.7738 (t80) cc_final: 0.7523 (t80) REVERT: B 356 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7836 (ptp90) outliers start: 31 outliers final: 16 residues processed: 88 average time/residue: 1.0832 time to fit residues: 103.3277 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 : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 280 SER 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 497 THR Chi-restraints excluded: chain A residue 523 GLU 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 417 VAL 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 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.115464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078702 restraints weight = 15041.819| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.79 r_work: 0.2919 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8811 Z= 0.209 Angle : 0.536 7.763 12151 Z= 0.276 Chirality : 0.041 0.137 1334 Planarity : 0.004 0.059 1399 Dihedral : 15.916 126.610 1424 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.70 % Rotamer: Outliers : 2.74 % Allowed : 31.07 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.28), residues: 944 helix: 1.62 (0.32), residues: 307 sheet: -0.71 (0.37), residues: 194 loop : -0.95 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.020 0.001 PHE B 87 TYR 0.035 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** 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 83 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8651 (mmt) cc_final: 0.8405 (mmm) REVERT: A 358 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8173 (mtp85) REVERT: A 373 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: A 535 TRP cc_start: 0.8418 (t60) cc_final: 0.7850 (t60) REVERT: B 192 ASP cc_start: 0.8811 (t0) cc_final: 0.8390 (m-30) REVERT: B 193 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 270 ILE cc_start: 0.8795 (tt) cc_final: 0.8531 (pt) REVERT: B 353 LYS cc_start: 0.9004 (tttp) cc_final: 0.8429 (ttmm) REVERT: B 356 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7827 (ptp90) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 1.0978 time to fit residues: 95.0060 Evaluate side-chains 75 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU 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 417 VAL 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 76 optimal weight: 0.6980 chunk 77 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.114482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077654 restraints weight = 16145.791| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.85 r_work: 0.2898 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8811 Z= 0.232 Angle : 0.549 8.892 12151 Z= 0.281 Chirality : 0.041 0.144 1334 Planarity : 0.004 0.064 1399 Dihedral : 15.900 126.809 1424 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 2.74 % Allowed : 31.31 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 944 helix: 1.63 (0.31), residues: 307 sheet: -0.68 (0.38), residues: 188 loop : -0.94 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE A 160 TYR 0.034 0.001 TYR A 457 ARG 0.008 0.001 ARG B 83 *********************** 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 80 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8708 (mmt) cc_final: 0.8439 (mmm) REVERT: A 358 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8176 (mtp85) REVERT: A 373 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6952 (mp10) REVERT: A 535 TRP cc_start: 0.8423 (t60) cc_final: 0.7898 (t60) REVERT: B 192 ASP cc_start: 0.8791 (t0) cc_final: 0.8434 (m-30) REVERT: B 193 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8770 (pp) REVERT: B 270 ILE cc_start: 0.8772 (tt) cc_final: 0.8529 (pt) REVERT: B 353 LYS cc_start: 0.9008 (tttp) cc_final: 0.8412 (ttmm) REVERT: B 354 TYR cc_start: 0.7665 (t80) cc_final: 0.7408 (t80) outliers start: 23 outliers final: 17 residues processed: 77 average time/residue: 1.0848 time to fit residues: 90.8030 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 : 1.009 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU 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 356 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.077500 restraints weight = 17831.404| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.00 r_work: 0.2891 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 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 = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 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 : 0.004 0.106 8811 Z= 0.234 Angle : 0.877 59.149 12151 Z= 0.503 Chirality : 0.041 0.244 1334 Planarity : 0.004 0.065 1399 Dihedral : 15.886 126.740 1422 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 2.50 % Allowed : 31.55 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 944 helix: 1.64 (0.31), residues: 307 sheet: -0.68 (0.37), residues: 188 loop : -0.93 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE B 87 TYR 0.033 0.001 TYR A 457 ARG 0.008 0.001 ARG A 358 ********************** 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 77 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8722 (mmt) cc_final: 0.8467 (mmm) REVERT: A 358 ARG cc_start: 0.8599 (mtp85) cc_final: 0.8195 (mtp85) REVERT: A 373 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: A 535 TRP cc_start: 0.8426 (t60) cc_final: 0.7808 (t60) REVERT: B 192 ASP cc_start: 0.8789 (t0) cc_final: 0.8431 (m-30) REVERT: B 193 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 270 ILE cc_start: 0.8774 (tt) cc_final: 0.8532 (pt) REVERT: B 353 LYS cc_start: 0.9013 (tttp) cc_final: 0.8416 (ttmm) REVERT: B 354 TYR cc_start: 0.7660 (t80) cc_final: 0.7406 (t80) outliers start: 21 outliers final: 15 residues processed: 74 average time/residue: 1.0930 time to fit residues: 87.5266 Evaluate side-chains 72 residues out of total 857 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 280 SER Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 523 GLU 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 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 92 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.0020 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077409 restraints weight = 18257.324| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.04 r_work: 0.2887 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- 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: 0.8683 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 8811 Z= 0.234 Angle : 0.877 59.148 12151 Z= 0.503 Chirality : 0.041 0.244 1334 Planarity : 0.004 0.065 1399 Dihedral : 15.886 126.740 1422 Min Nonbonded Distance : 1.024 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 2.14 % Allowed : 31.79 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 944 helix: 1.64 (0.31), residues: 307 sheet: -0.68 (0.37), residues: 188 loop : -0.93 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 414 HIS 0.003 0.001 HIS B 208 PHE 0.010 0.001 PHE B 87 TYR 0.033 0.001 TYR A 457 ARG 0.008 0.001 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5654.33 seconds wall clock time: 100 minutes 59.21 seconds (6059.21 seconds total)