Starting phenix.real_space_refine on Thu Nov 14 23:00:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_16794.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_16794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_16794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_16794.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cqb_16794/11_2024/8cqb_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.89, per 1000 atoms: 0.64 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: 2.56 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: 0.94 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: 4.10 Time building geometry restraints manager: 2.43 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: 0.00 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: 2.710 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- 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 : 0.917 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: 0.2439 time to fit residues: 39.8372 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 : 0.866 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 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 : 0.862 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: 0.6030 (t80) cc_final: 0.5812 (t80) REVERT: B 162 GLU cc_start: -0.1004 (OUTLIER) cc_final: -0.3589 (mm-30) REVERT: B 334 HIS cc_start: 0.8115 (t70) cc_final: 0.7794 (t70) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.2281 time to fit residues: 38.0341 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 : 0.917 ------------------------------------------------------------------------------- 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 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 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 16 ASN B 16 ASN B 276 ASN B 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7834 Z= 0.193 Angle : 0.637 9.847 10590 Z= 0.315 Chirality : 0.041 0.216 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.693 135.344 1042 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.20 % Favored : 93.38 % Rotamer: Outliers : 2.82 % Allowed : 25.94 % Favored : 71.24 % 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: 1.07 (0.23), residues: 493 sheet: 0.84 (0.48), residues: 98 loop : -1.93 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.009 0.001 HIS B 334 PHE 0.023 0.002 PHE B 219 TYR 0.018 0.001 TYR B 47 ARG 0.005 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 130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.928 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: 0.5994 (t80) cc_final: 0.5462 (t80) REVERT: B 101 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7821 (mt) REVERT: B 112 ASP cc_start: 0.6857 (t0) cc_final: 0.6399 (t0) REVERT: B 139 MET cc_start: 0.7826 (mmt) cc_final: 0.7297 (tpp) REVERT: B 162 GLU cc_start: -0.1252 (OUTLIER) cc_final: -0.3724 (mm-30) REVERT: B 334 HIS cc_start: 0.8067 (t70) cc_final: 0.7805 (t70) outliers start: 24 outliers final: 6 residues processed: 126 average time/residue: 0.2462 time to fit residues: 40.9142 Evaluate side-chains 102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 101 LEU 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 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7834 Z= 0.324 Angle : 0.704 10.400 10590 Z= 0.349 Chirality : 0.044 0.235 1182 Planarity : 0.005 0.052 1358 Dihedral : 9.237 127.559 1042 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.72 % Favored : 92.86 % Rotamer: Outliers : 2.93 % Allowed : 25.70 % Favored : 71.36 % 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: -0.34 (0.27), residues: 952 helix: 0.96 (0.23), residues: 494 sheet: -0.04 (0.47), residues: 98 loop : -2.00 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 180 HIS 0.009 0.001 HIS B 334 PHE 0.022 0.002 PHE A 230 TYR 0.019 0.002 TYR A 47 ARG 0.011 0.001 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 120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.900 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: 0.6336 (t80) cc_final: 0.5363 (t80) REVERT: B 8 THR cc_start: 0.5615 (OUTLIER) cc_final: 0.5149 (t) REVERT: B 101 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8011 (mt) REVERT: B 139 MET cc_start: 0.7972 (mmt) cc_final: 0.7474 (tpp) REVERT: B 334 HIS cc_start: 0.8063 (t70) cc_final: 0.7773 (t70) outliers start: 25 outliers final: 9 residues processed: 116 average time/residue: 0.2600 time to fit residues: 39.0776 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 : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7834 Z= 0.221 Angle : 0.651 9.951 10590 Z= 0.320 Chirality : 0.042 0.148 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.858 130.272 1042 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.20 % Favored : 93.38 % Rotamer: Outliers : 2.93 % Allowed : 25.59 % 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: -0.18 (0.27), residues: 952 helix: 1.11 (0.23), residues: 494 sheet: 0.19 (0.48), residues: 98 loop : -2.01 (0.32), residues: 360 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 368 TYR 0.031 0.002 TYR A 47 ARG 0.007 0.001 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 124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.808 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 216 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.5959 (t0) REVERT: A 229 PHE cc_start: 0.6281 (t80) cc_final: 0.5338 (t80) REVERT: B 112 ASP cc_start: 0.7203 (t0) cc_final: 0.6726 (t0) REVERT: B 139 MET cc_start: 0.7948 (mmt) cc_final: 0.7527 (tpp) REVERT: B 334 HIS cc_start: 0.8065 (t70) cc_final: 0.7799 (t70) outliers start: 25 outliers final: 14 residues processed: 119 average time/residue: 0.2456 time to fit residues: 38.3125 Evaluate side-chains 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 216 ASP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 101 LEU 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 437 VAL Chi-restraints excluded: chain B residue 438 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7834 Z= 0.282 Angle : 0.698 10.331 10590 Z= 0.339 Chirality : 0.043 0.147 1182 Planarity : 0.004 0.049 1358 Dihedral : 9.025 129.577 1042 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.46 % Favored : 92.12 % Rotamer: Outliers : 2.93 % Allowed : 26.41 % Favored : 70.66 % 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: -0.19 (0.28), residues: 952 helix: 1.07 (0.23), residues: 495 sheet: -0.10 (0.50), residues: 94 loop : -1.85 (0.33), residues: 363 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 0.017 0.002 PHE A 373 TYR 0.028 0.002 TYR A 47 ARG 0.007 0.001 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 112 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.938 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 216 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6002 (t0) REVERT: A 229 PHE cc_start: 0.6325 (t80) cc_final: 0.5341 (t80) REVERT: B 38 MET cc_start: 0.5862 (ptt) cc_final: 0.5649 (ptt) REVERT: B 101 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7962 (mt) REVERT: B 139 MET cc_start: 0.7996 (mmt) cc_final: 0.7575 (tpp) REVERT: B 334 HIS cc_start: 0.8079 (t70) cc_final: 0.7837 (t70) REVERT: B 338 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8230 (mp10) outliers start: 25 outliers final: 12 residues processed: 110 average time/residue: 0.2482 time to fit residues: 35.7877 Evaluate side-chains 96 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 216 ASP Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 101 LEU 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 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 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7834 Z= 0.207 Angle : 0.663 10.373 10590 Z= 0.323 Chirality : 0.042 0.181 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.684 130.848 1042 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.30 % Favored : 93.28 % Rotamer: Outliers : 2.46 % Allowed : 27.23 % Favored : 70.31 % 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: -0.09 (0.27), residues: 952 helix: 1.18 (0.23), residues: 490 sheet: 0.16 (0.50), residues: 94 loop : -1.88 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.007 0.001 HIS B 334 PHE 0.018 0.002 PHE B 436 TYR 0.022 0.002 TYR A 47 ARG 0.005 0.000 ARG A 370 *********************** 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 117 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.781 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: B 112 ASP cc_start: 0.7050 (t0) cc_final: 0.6568 (t0) REVERT: B 139 MET cc_start: 0.7964 (mmt) cc_final: 0.7567 (tpp) REVERT: B 334 HIS cc_start: 0.7979 (t70) cc_final: 0.7759 (t70) REVERT: B 338 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8227 (mp10) outliers start: 21 outliers final: 14 residues processed: 114 average time/residue: 0.2262 time to fit residues: 34.2672 Evaluate side-chains 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 271 SER Chi-restraints excluded: chain B residue 101 LEU 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 420 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7834 Z= 0.334 Angle : 0.749 12.323 10590 Z= 0.362 Chirality : 0.045 0.181 1182 Planarity : 0.005 0.049 1358 Dihedral : 9.128 129.166 1042 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.88 % Favored : 91.70 % Rotamer: Outliers : 2.23 % Allowed : 27.82 % 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: -0.36 (0.27), residues: 952 helix: 0.99 (0.23), residues: 490 sheet: -0.48 (0.51), residues: 95 loop : -1.88 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.010 0.002 HIS B 378 PHE 0.017 0.002 PHE A 373 TYR 0.026 0.002 TYR A 47 ARG 0.005 0.001 ARG A 153 *********************** 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 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.952 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: 0.6496 (t80) cc_final: 0.5486 (t80) REVERT: B 55 MET cc_start: 0.7743 (mmm) cc_final: 0.7354 (mmm) REVERT: B 101 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 139 MET cc_start: 0.8022 (mmt) cc_final: 0.7637 (tpp) REVERT: B 334 HIS cc_start: 0.8045 (t70) cc_final: 0.7766 (t70) REVERT: B 338 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8220 (mp10) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.2292 time to fit residues: 31.9003 Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 271 SER Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN B 16 ASN ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7834 Z= 0.336 Angle : 0.764 12.695 10590 Z= 0.368 Chirality : 0.045 0.173 1182 Planarity : 0.005 0.049 1358 Dihedral : 9.200 127.002 1042 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.14 % Favored : 92.44 % Rotamer: Outliers : 2.70 % Allowed : 27.70 % Favored : 69.60 % 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: -0.50 (0.27), residues: 952 helix: 0.89 (0.23), residues: 489 sheet: -0.64 (0.52), residues: 93 loop : -1.94 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.007 0.001 HIS B 378 PHE 0.020 0.002 PHE A 373 TYR 0.026 0.002 TYR A 47 ARG 0.008 0.001 ARG A 151 *********************** 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 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.971 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 161 ASN cc_start: 0.5797 (OUTLIER) cc_final: 0.5501 (t0) REVERT: B 55 MET cc_start: 0.7743 (mmm) cc_final: 0.7341 (mmm) REVERT: B 139 MET cc_start: 0.7997 (mmt) cc_final: 0.7624 (tpp) REVERT: B 334 HIS cc_start: 0.8020 (t70) cc_final: 0.7766 (t70) REVERT: B 338 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8227 (mp10) outliers start: 23 outliers final: 16 residues processed: 103 average time/residue: 0.2119 time to fit residues: 30.0384 Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 161 ASN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 SER 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 204 TYR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 7 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 HIS ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7834 Z= 0.187 Angle : 0.711 11.290 10590 Z= 0.342 Chirality : 0.043 0.191 1182 Planarity : 0.004 0.048 1358 Dihedral : 8.569 126.653 1042 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.62 % Favored : 92.96 % Rotamer: Outliers : 1.41 % Allowed : 29.23 % Favored : 69.37 % 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: -0.30 (0.27), residues: 952 helix: 1.02 (0.23), residues: 491 sheet: -0.24 (0.51), residues: 94 loop : -1.91 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.007 0.001 HIS B 334 PHE 0.031 0.002 PHE B 368 TYR 0.020 0.001 TYR A 47 ARG 0.007 0.001 ARG A 151 ********************** 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 113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.867 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 339 MET cc_start: 0.7063 (mmp) cc_final: 0.5987 (tpp) REVERT: B 139 MET cc_start: 0.7933 (mmt) cc_final: 0.7496 (tpp) REVERT: B 322 ILE cc_start: 0.6896 (mm) cc_final: 0.6518 (mm) REVERT: B 338 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8219 (mp10) outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.2170 time to fit residues: 32.5541 Evaluate side-chains 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 420 GLU Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS B 399 ASN ** 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 = 0.4310 r_free = 0.4310 target = 0.180302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147130 restraints weight = 10406.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152468 restraints weight = 16170.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153630 restraints weight = 8261.196| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7834 Z= 0.221 Angle : 0.732 11.016 10590 Z= 0.352 Chirality : 0.043 0.217 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.648 129.991 1042 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.20 % Favored : 93.38 % Rotamer: Outliers : 1.53 % Allowed : 29.34 % Favored : 69.13 % 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: -0.19 (0.27), residues: 952 helix: 1.08 (0.23), residues: 492 sheet: 0.12 (0.51), residues: 96 loop : -1.92 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.015 0.001 HIS B 334 PHE 0.024 0.002 PHE A 373 TYR 0.021 0.002 TYR A 47 ARG 0.007 0.001 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.45 seconds wall clock time: 33 minutes 34.41 seconds (2014.41 seconds total)