Starting phenix.real_space_refine on Wed Feb 12 09:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqb_16794/02_2025/8cqb_16794.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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: 8 Type Number sf(0) Gaussians Al 2 5.89 5 P 4 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 4860 2.51 5 N 1292 2.21 5 O 1486 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3811 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} Chain: "B" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3811 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 20, 'TRANS': 457} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.76 Number of scatterers: 7688 At special positions: 0 Unit cell: (70.89, 95.076, 150.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 36 16.00 P 4 15.00 Al 2 13.00 Mg 2 11.99 F 6 9.00 O 1486 8.00 N 1292 7.00 C 4860 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 57.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.795A pdb=" N ILE A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.717A pdb=" N ASP A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.924A pdb=" N SER A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'A' and resid 213 through 230 removed outlier: 3.539A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 259 through 277 removed outlier: 3.524A pdb=" N VAL A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 305 Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.515A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 342 Processing helix chain 'A' and resid 350 through 372 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 424 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 432 through 450 removed outlier: 4.046A pdb=" N PHE A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.784A pdb=" N ALA A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ILE A 475 " --> pdb=" O MET A 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.629A pdb=" N ILE B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 removed outlier: 3.580A pdb=" N LYS B 57 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 123 removed outlier: 3.693A pdb=" N ASP B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.606A pdb=" N GLU B 147 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.757A pdb=" N SER B 173 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 213 through 230 Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 289 through 305 Processing helix chain 'B' and resid 316 through 341 Processing helix chain 'B' and resid 349 through 372 removed outlier: 5.117A pdb=" N GLU B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 378 through 415 Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.538A pdb=" N LYS B 429 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.769A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 473 removed outlier: 3.671A pdb=" N LEU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.741A pdb=" N LEU B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.922A pdb=" N ILE A 78 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 39 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 96 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 41 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR A 98 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A 43 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 178 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N PHE A 236 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP A 180 " --> pdb=" O PHE A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.658A pdb=" N MET B 22 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 78 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 39 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU B 96 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 41 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR B 98 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45 removed outlier: 8.486A pdb=" N PHE B 236 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP B 180 " --> pdb=" O PHE B 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 191 418 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2514 1.34 - 1.46: 1582 1.46 - 1.58: 3673 1.58 - 1.69: 3 1.69 - 1.81: 62 Bond restraints: 7834 Sorted by residual: bond pdb=" F3 AF3 A 602 " pdb="AL AF3 A 602 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F1 AF3 A 602 " pdb="AL AF3 A 602 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F3 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.707 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" F2 AF3 A 602 " pdb="AL AF3 A 602 " ideal model delta sigma weight residual 1.637 1.706 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" F1 AF3 B 602 " pdb="AL AF3 B 602 " ideal model delta sigma weight residual 1.637 1.706 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 7829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 10432 2.14 - 4.28: 126 4.28 - 6.42: 23 6.42 - 8.56: 4 8.56 - 10.71: 5 Bond angle restraints: 10590 Sorted by residual: angle pdb=" O5' GDP A 601 " pdb=" PA GDP A 601 " pdb=" O2A GDP A 601 " ideal model delta sigma weight residual 109.50 98.79 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C LYS A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C3' GDP A 601 " pdb=" C2' GDP A 601 " pdb=" C1' GDP A 601 " ideal model delta sigma weight residual 111.00 100.58 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C LYS B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" O3A GDP A 601 " pdb=" PB GDP A 601 " pdb=" O3B GDP A 601 " ideal model delta sigma weight residual 109.50 100.17 9.33 3.00e+00 1.11e-01 9.67e+00 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 4310 24.80 - 49.61: 409 49.61 - 74.41: 51 74.41 - 99.21: 16 99.21 - 124.01: 2 Dihedral angle restraints: 4788 sinusoidal: 1988 harmonic: 2800 Sorted by residual: dihedral pdb=" O2B GDP A 601 " pdb=" O3A GDP A 601 " pdb=" PB GDP A 601 " pdb=" PA GDP A 601 " ideal model delta sinusoidal sigma weight residual -180.00 -55.99 -124.01 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O2B GDP B 601 " pdb=" O3A GDP B 601 " pdb=" PB GDP B 601 " pdb=" PA GDP B 601 " ideal model delta sinusoidal sigma weight residual -180.00 -78.27 -101.73 1 2.00e+01 2.50e-03 2.89e+01 dihedral pdb=" O4' GDP A 601 " pdb=" C1' GDP A 601 " pdb=" N9 GDP A 601 " pdb=" C8 GDP A 601 " ideal model delta sinusoidal sigma weight residual 27.02 119.09 -92.07 1 2.00e+01 2.50e-03 2.49e+01 ... (remaining 4785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 746 0.028 - 0.055: 272 0.055 - 0.083: 83 0.083 - 0.110: 64 0.110 - 0.138: 17 Chirality restraints: 1182 Sorted by residual: chirality pdb=" C3' GDP A 601 " pdb=" C4' GDP A 601 " pdb=" O3' GDP A 601 " pdb=" C2' GDP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA LYS A 210 " pdb=" N LYS A 210 " pdb=" C LYS A 210 " pdb=" CB LYS A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL B 179 " pdb=" N VAL B 179 " pdb=" C VAL B 179 " pdb=" CB VAL B 179 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1179 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 197 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 198 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 230 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 231 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 231 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 231 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 36 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 37 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 37 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 37 " -0.022 5.00e-02 4.00e+02 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 3 1.93 - 2.68: 174 2.68 - 3.42: 11489 3.42 - 4.16: 18100 4.16 - 4.90: 32865 Nonbonded interactions: 62631 Sorted by model distance: nonbonded pdb=" O2B GDP A 601 " pdb="MG MG A 603 " model vdw 1.193 2.170 nonbonded pdb=" O1B GDP A 601 " pdb=" F2 AF3 A 602 " model vdw 1.892 2.990 nonbonded pdb=" O3B GDP B 601 " pdb=" F3 AF3 B 602 " model vdw 1.912 2.990 nonbonded pdb=" OG1 THR B 75 " pdb="MG MG B 603 " model vdw 1.952 2.170 nonbonded pdb=" OG SER B 52 " pdb="MG MG B 603 " model vdw 1.953 2.170 ... (remaining 62626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 : 0.003 0.071 7834 Z= 0.222 Angle : 0.635 10.705 10590 Z= 0.304 Chirality : 0.039 0.138 1182 Planarity : 0.004 0.048 1358 Dihedral : 18.673 124.013 2972 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.49 % Rotamer: Outliers : 1.29 % Allowed : 24.53 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.27), residues: 952 helix: 0.64 (0.23), residues: 494 sheet: 0.62 (0.47), residues: 98 loop : -1.88 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 114 HIS 0.005 0.001 HIS B 334 PHE 0.014 0.001 PHE A 219 TYR 0.015 0.001 TYR B 47 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 MET cc_start: 0.7641 (ppp) cc_final: 0.6989 (ppp) REVERT: B 334 HIS cc_start: 0.8128 (t70) cc_final: 0.7839 (t70) REVERT: B 358 ARG cc_start: 0.7899 (tpm170) cc_final: 0.7677 (tpm170) outliers start: 11 outliers final: 2 residues processed: 126 average time/residue: 0.2411 time to fit residues: 39.4135 Evaluate side-chains 97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 70 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.0050 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 111 ASN B 302 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.133848 restraints weight = 10368.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137063 restraints weight = 7531.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139093 restraints weight = 6162.565| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7834 Z= 0.268 Angle : 0.679 9.936 10590 Z= 0.334 Chirality : 0.043 0.214 1182 Planarity : 0.004 0.049 1358 Dihedral : 9.134 133.937 1044 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.41 % Favored : 93.17 % Rotamer: Outliers : 1.64 % Allowed : 25.82 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.27), residues: 952 helix: 0.86 (0.23), residues: 499 sheet: 0.66 (0.47), residues: 98 loop : -1.96 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.008 0.001 HIS B 334 PHE 0.020 0.002 PHE A 373 TYR 0.019 0.002 TYR B 47 ARG 0.003 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6064 (t80) cc_final: 0.5832 (t80) REVERT: B 162 GLU cc_start: -0.1176 (OUTLIER) cc_final: -0.3684 (mm-30) REVERT: B 334 HIS cc_start: 0.8146 (t70) cc_final: 0.7828 (t70) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.2251 time to fit residues: 37.5494 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 64 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN B 16 ASN B 276 ASN B 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.181480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.145451 restraints weight = 10505.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149986 restraints weight = 16118.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.150877 restraints weight = 9535.577| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7834 Z= 0.213 Angle : 0.646 9.800 10590 Z= 0.319 Chirality : 0.042 0.229 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.801 134.581 1042 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.99 % Favored : 93.59 % Rotamer: Outliers : 2.82 % Allowed : 26.29 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.27), residues: 952 helix: 1.05 (0.23), residues: 493 sheet: 0.70 (0.48), residues: 98 loop : -1.95 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.008 0.001 HIS B 334 PHE 0.022 0.002 PHE B 219 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6083 (t80) cc_final: 0.5519 (t80) REVERT: B 112 ASP cc_start: 0.6999 (t0) cc_final: 0.6658 (t0) REVERT: B 139 MET cc_start: 0.7878 (mmt) cc_final: 0.7460 (tpp) REVERT: B 162 GLU cc_start: -0.1412 (OUTLIER) cc_final: -0.3838 (mm-30) outliers start: 24 outliers final: 6 residues processed: 121 average time/residue: 0.2490 time to fit residues: 39.4042 Evaluate side-chains 97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 16 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135434 restraints weight = 10519.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136897 restraints weight = 8630.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136937 restraints weight = 6512.617| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7834 Z= 0.225 Angle : 0.646 9.500 10590 Z= 0.319 Chirality : 0.042 0.193 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.735 130.057 1042 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.62 % Favored : 92.96 % Rotamer: Outliers : 2.11 % Allowed : 26.41 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 952 helix: 1.13 (0.23), residues: 494 sheet: 0.50 (0.48), residues: 98 loop : -1.93 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 114 HIS 0.016 0.001 HIS B 334 PHE 0.018 0.002 PHE B 219 TYR 0.015 0.002 TYR A 47 ARG 0.010 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6121 (t80) cc_final: 0.5195 (t80) REVERT: B 8 THR cc_start: 0.5586 (OUTLIER) cc_final: 0.5089 (t) REVERT: B 139 MET cc_start: 0.7875 (mmt) cc_final: 0.7406 (tpp) REVERT: B 162 GLU cc_start: -0.1191 (OUTLIER) cc_final: -0.3916 (mm-30) REVERT: B 229 PHE cc_start: 0.6969 (t80) cc_final: 0.6756 (t80) outliers start: 18 outliers final: 11 residues processed: 117 average time/residue: 0.2478 time to fit residues: 37.7524 Evaluate side-chains 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 66 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 400 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 = 0.4327 r_free = 0.4327 target = 0.182518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.135585 restraints weight = 10427.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138703 restraints weight = 7618.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140568 restraints weight = 6174.749| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7834 Z= 0.181 Angle : 0.632 10.742 10590 Z= 0.307 Chirality : 0.041 0.152 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.453 132.570 1042 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.49 % Rotamer: Outliers : 2.58 % Allowed : 26.53 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.27), residues: 952 helix: 1.23 (0.23), residues: 494 sheet: 0.78 (0.51), residues: 94 loop : -1.90 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 114 HIS 0.014 0.001 HIS B 334 PHE 0.016 0.002 PHE B 219 TYR 0.015 0.001 TYR B 47 ARG 0.007 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6166 (t80) cc_final: 0.5259 (t80) REVERT: A 257 GLU cc_start: 0.4653 (mp0) cc_final: 0.4187 (mp0) REVERT: B 8 THR cc_start: 0.5280 (OUTLIER) cc_final: 0.4804 (t) REVERT: B 139 MET cc_start: 0.7842 (mmt) cc_final: 0.7467 (tpp) REVERT: B 162 GLU cc_start: -0.1321 (OUTLIER) cc_final: -0.3912 (mm-30) REVERT: B 229 PHE cc_start: 0.7039 (t80) cc_final: 0.6771 (t80) outliers start: 22 outliers final: 12 residues processed: 126 average time/residue: 0.2566 time to fit residues: 42.5201 Evaluate side-chains 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 400 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 = 0.4324 r_free = 0.4324 target = 0.182244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145326 restraints weight = 10294.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148844 restraints weight = 15881.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149937 restraints weight = 10862.667| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7834 Z= 0.204 Angle : 0.643 10.011 10590 Z= 0.312 Chirality : 0.041 0.161 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.510 133.650 1042 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.99 % Favored : 93.59 % Rotamer: Outliers : 2.70 % Allowed : 26.76 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.28), residues: 952 helix: 1.24 (0.23), residues: 493 sheet: 0.62 (0.51), residues: 95 loop : -1.71 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.013 0.001 HIS B 334 PHE 0.016 0.002 PHE A 368 TYR 0.014 0.001 TYR B 47 ARG 0.005 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6346 (t80) cc_final: 0.5453 (t80) REVERT: B 8 THR cc_start: 0.5456 (OUTLIER) cc_final: 0.4937 (t) REVERT: B 139 MET cc_start: 0.7918 (mmt) cc_final: 0.7622 (tpp) REVERT: B 229 PHE cc_start: 0.6988 (t80) cc_final: 0.6747 (t80) REVERT: B 338 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8226 (mp10) outliers start: 23 outliers final: 13 residues processed: 121 average time/residue: 0.2404 time to fit residues: 37.7473 Evaluate side-chains 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** B 400 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 = 0.4293 r_free = 0.4293 target = 0.179045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.142214 restraints weight = 10429.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145040 restraints weight = 16280.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146389 restraints weight = 11879.744| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7834 Z= 0.258 Angle : 0.677 10.091 10590 Z= 0.330 Chirality : 0.043 0.189 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.788 132.733 1042 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.30 % Favored : 93.28 % Rotamer: Outliers : 2.35 % Allowed : 28.17 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.28), residues: 952 helix: 1.23 (0.23), residues: 490 sheet: 0.35 (0.49), residues: 97 loop : -1.76 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.013 0.001 HIS B 334 PHE 0.019 0.002 PHE A 373 TYR 0.015 0.002 TYR A 47 ARG 0.007 0.001 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6137 (tpp80) cc_final: 0.5887 (tpp80) REVERT: A 229 PHE cc_start: 0.6445 (t80) cc_final: 0.5542 (t80) REVERT: B 139 MET cc_start: 0.7969 (mmt) cc_final: 0.7666 (tpp) REVERT: B 229 PHE cc_start: 0.7083 (t80) cc_final: 0.6820 (t80) REVERT: B 338 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (mp10) outliers start: 20 outliers final: 13 residues processed: 112 average time/residue: 0.2505 time to fit residues: 36.6339 Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 ASN B 378 HIS ** B 400 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 = 0.4339 r_free = 0.4339 target = 0.183152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.146611 restraints weight = 10486.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.151245 restraints weight = 14534.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152026 restraints weight = 10444.759| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7834 Z= 0.173 Angle : 0.654 10.417 10590 Z= 0.318 Chirality : 0.042 0.171 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.418 132.808 1042 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.49 % Rotamer: Outliers : 2.00 % Allowed : 28.05 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.28), residues: 952 helix: 1.31 (0.23), residues: 490 sheet: 0.76 (0.50), residues: 97 loop : -1.70 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.014 0.001 HIS B 334 PHE 0.022 0.002 PHE A 373 TYR 0.017 0.001 TYR B 53 ARG 0.008 0.001 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6428 (t80) cc_final: 0.5583 (t80) REVERT: B 139 MET cc_start: 0.7933 (mmt) cc_final: 0.7672 (tpp) REVERT: B 229 PHE cc_start: 0.7072 (t80) cc_final: 0.6777 (t80) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.2413 time to fit residues: 36.0556 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS ** B 400 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 = 0.4330 r_free = 0.4330 target = 0.182374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145770 restraints weight = 10460.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.150277 restraints weight = 14653.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151112 restraints weight = 10127.270| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7834 Z= 0.200 Angle : 0.663 10.463 10590 Z= 0.324 Chirality : 0.042 0.165 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.505 133.783 1042 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.99 % Favored : 93.59 % Rotamer: Outliers : 1.64 % Allowed : 28.29 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.28), residues: 952 helix: 1.37 (0.23), residues: 490 sheet: 0.78 (0.50), residues: 97 loop : -1.68 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 114 HIS 0.016 0.001 HIS B 334 PHE 0.018 0.002 PHE A 373 TYR 0.015 0.002 TYR B 53 ARG 0.013 0.001 ARG B 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 PHE cc_start: 0.6461 (t80) cc_final: 0.5590 (t80) REVERT: B 139 MET cc_start: 0.7931 (mmt) cc_final: 0.7681 (tpp) REVERT: B 229 PHE cc_start: 0.7058 (t80) cc_final: 0.6764 (t80) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.2270 time to fit residues: 31.9703 Evaluate side-chains 102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133853 restraints weight = 10575.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136795 restraints weight = 8074.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.137676 restraints weight = 7178.526| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7834 Z= 0.211 Angle : 0.688 11.117 10590 Z= 0.335 Chirality : 0.043 0.204 1182 Planarity : 0.005 0.054 1358 Dihedral : 8.532 134.340 1042 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.49 % Rotamer: Outliers : 1.29 % Allowed : 28.76 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.28), residues: 952 helix: 1.30 (0.23), residues: 490 sheet: 0.72 (0.50), residues: 97 loop : -1.65 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 114 HIS 0.009 0.001 HIS B 378 PHE 0.021 0.002 PHE A 368 TYR 0.015 0.002 TYR B 47 ARG 0.014 0.001 ARG B 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.8429 (pmm) cc_final: 0.8228 (pmm) REVERT: A 229 PHE cc_start: 0.6436 (t80) cc_final: 0.5519 (t80) REVERT: B 139 MET cc_start: 0.7958 (mmt) cc_final: 0.7584 (tpp) REVERT: B 229 PHE cc_start: 0.7161 (t80) cc_final: 0.6784 (t80) REVERT: B 339 MET cc_start: 0.7589 (mmt) cc_final: 0.7021 (mmm) outliers start: 11 outliers final: 11 residues processed: 102 average time/residue: 0.2403 time to fit residues: 32.3206 Evaluate side-chains 98 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.181158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132975 restraints weight = 10504.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136988 restraints weight = 7942.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138043 restraints weight = 6607.220| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7834 Z= 0.227 Angle : 0.713 13.851 10590 Z= 0.347 Chirality : 0.043 0.252 1182 Planarity : 0.005 0.054 1358 Dihedral : 8.620 134.651 1042 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.41 % Favored : 93.17 % Rotamer: Outliers : 1.53 % Allowed : 28.76 % Favored : 69.72 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.28), residues: 952 helix: 1.25 (0.23), residues: 490 sheet: 0.62 (0.50), residues: 97 loop : -1.68 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 114 HIS 0.007 0.001 HIS B 334 PHE 0.020 0.002 PHE A 373 TYR 0.015 0.002 TYR B 47 ARG 0.014 0.001 ARG B 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.21 seconds wall clock time: 44 minutes 48.93 seconds (2688.93 seconds total)