Starting phenix.real_space_refine on Wed Mar 12 09:43:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cqb_16794/03_2025/8cqb_16794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cqb_16794/03_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_16794/03_2025/8cqb_16794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cqb_16794/03_2025/8cqb_16794.map" model { file = "/net/cci-nas-00/data/ceres_data/8cqb_16794/03_2025/8cqb_16794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cqb_16794/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.43, per 1000 atoms: 0.71 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: 1.90 Conformation dependent library (CDL) restraints added in 1.0 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: 0.73 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: 1.99 Time building geometry restraints manager: 2.21 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: 1.540 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.270 Find NCS groups from input model: 0.270 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- 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 : 0.851 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: 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: 0.2386 time to fit residues: 39.0926 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 : 0.915 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.133774 restraints weight = 10368.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136942 restraints weight = 7565.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139201 restraints weight = 6185.182| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 : 0.880 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: 0.5835 (t80) REVERT: B 162 GLU cc_start: -0.1181 (OUTLIER) cc_final: -0.3686 (mm-30) REVERT: B 334 HIS cc_start: 0.8145 (t70) cc_final: 0.7826 (t70) outliers start: 14 outliers final: 8 residues processed: 126 average time/residue: 0.2200 time to fit residues: 36.8486 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 : 0.845 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.4320 r_free = 0.4320 target = 0.181896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145960 restraints weight = 10500.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.150540 restraints weight = 15984.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.151411 restraints weight = 9511.593| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7834 Z= 0.205 Angle : 0.642 9.784 10590 Z= 0.317 Chirality : 0.042 0.227 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.755 134.720 1042 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.09 % Favored : 93.49 % Rotamer: Outliers : 2.70 % Allowed : 26.29 % Favored : 71.01 % 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: -0.10 (0.27), residues: 952 helix: 1.06 (0.23), residues: 493 sheet: 0.75 (0.48), residues: 98 loop : -1.94 (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 0.022 0.002 PHE B 219 TYR 0.017 0.001 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 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.366 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: 0.6093 (t80) cc_final: 0.5473 (t80) REVERT: B 101 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 112 ASP cc_start: 0.6973 (t0) cc_final: 0.6458 (t0) REVERT: B 139 MET cc_start: 0.7874 (mmt) cc_final: 0.7441 (tpp) REVERT: B 162 GLU cc_start: -0.1399 (OUTLIER) cc_final: -0.3821 (mm-30) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 0.2442 time to fit residues: 39.2989 Evaluate side-chains 98 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 16 ASN 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 39 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131485 restraints weight = 10568.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134285 restraints weight = 7855.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136359 restraints weight = 6489.675| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7834 Z= 0.275 Angle : 0.672 9.623 10590 Z= 0.332 Chirality : 0.043 0.204 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.953 129.446 1042 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.83 % Favored : 92.75 % Rotamer: Outliers : 2.58 % Allowed : 26.06 % 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: -0.18 (0.27), residues: 952 helix: 1.06 (0.23), residues: 494 sheet: 0.25 (0.47), residues: 98 loop : -1.94 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 114 HIS 0.017 0.001 HIS B 334 PHE 0.018 0.002 PHE B 219 TYR 0.016 0.002 TYR A 47 ARG 0.010 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 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 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: 0.6255 (t80) cc_final: 0.5349 (t80) REVERT: B 8 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.4888 (t) REVERT: B 101 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 112 ASP cc_start: 0.7005 (t0) cc_final: 0.6628 (t0) REVERT: B 139 MET cc_start: 0.7935 (mmt) cc_final: 0.7444 (tpp) REVERT: B 229 PHE cc_start: 0.7022 (t80) cc_final: 0.6809 (t80) outliers start: 22 outliers final: 12 residues processed: 119 average time/residue: 0.2313 time to fit residues: 36.3303 Evaluate side-chains 104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 270 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 22 MET 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 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: 0.8980 chunk 30 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.181364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134251 restraints weight = 10442.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.137161 restraints weight = 7710.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139294 restraints weight = 6315.770| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7834 Z= 0.192 Angle : 0.642 10.021 10590 Z= 0.314 Chirality : 0.042 0.165 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.647 132.001 1042 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.78 % Favored : 93.80 % 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: 0.02 (0.27), residues: 952 helix: 1.25 (0.23), residues: 488 sheet: 0.53 (0.49), residues: 94 loop : -1.87 (0.32), residues: 370 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 0.024 0.002 PHE B 219 TYR 0.016 0.002 TYR B 47 ARG 0.006 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 122 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 2.370 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: 0.6202 (t80) cc_final: 0.5331 (t80) REVERT: B 8 THR cc_start: 0.5248 (OUTLIER) cc_final: 0.4761 (t) REVERT: B 112 ASP cc_start: 0.6978 (t0) cc_final: 0.6509 (t0) REVERT: B 139 MET cc_start: 0.7929 (mmt) cc_final: 0.7456 (tpp) REVERT: B 229 PHE cc_start: 0.7051 (t80) cc_final: 0.6784 (t80) outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.4256 time to fit residues: 69.5983 Evaluate side-chains 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 293 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 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 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 = 0.4317 r_free = 0.4317 target = 0.181316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145207 restraints weight = 10352.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148762 restraints weight = 15869.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149834 restraints weight = 10845.517| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7834 Z= 0.208 Angle : 0.649 10.021 10590 Z= 0.316 Chirality : 0.041 0.163 1182 Planarity : 0.004 0.050 1358 Dihedral : 8.634 133.353 1042 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.99 % Favored : 93.59 % Rotamer: Outliers : 3.17 % Allowed : 25.82 % Favored : 71.01 % 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 (0.28), residues: 952 helix: 1.22 (0.23), residues: 493 sheet: 0.53 (0.49), residues: 94 loop : -1.78 (0.33), 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 0.020 0.002 PHE B 219 TYR 0.015 0.002 TYR B 47 ARG 0.006 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 127 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.859 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: 0.6256 (t80) cc_final: 0.5389 (t80) REVERT: B 112 ASP cc_start: 0.7156 (t0) cc_final: 0.6849 (t0) REVERT: B 139 MET cc_start: 0.7962 (mmt) cc_final: 0.7596 (tpp) REVERT: B 229 PHE cc_start: 0.7001 (t80) cc_final: 0.6737 (t80) REVERT: B 338 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8191 (mp10) outliers start: 27 outliers final: 14 residues processed: 124 average time/residue: 0.2414 time to fit residues: 39.0387 Evaluate side-chains 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 A residue 319 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4267 r_free = 0.4267 target = 0.176752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130467 restraints weight = 10468.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132055 restraints weight = 9430.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.132562 restraints weight = 7721.901| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2893 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= 0.336 Angle : 0.734 10.564 10590 Z= 0.360 Chirality : 0.045 0.227 1182 Planarity : 0.005 0.050 1358 Dihedral : 9.116 129.227 1042 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.04 % Favored : 92.54 % Rotamer: Outliers : 2.46 % Allowed : 27.00 % 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: -0.19 (0.28), residues: 952 helix: 1.11 (0.23), residues: 491 sheet: -0.26 (0.50), residues: 94 loop : -1.83 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 180 HIS 0.012 0.001 HIS B 334 PHE 0.021 0.002 PHE A 373 TYR 0.018 0.002 TYR A 47 ARG 0.006 0.001 ARG A 153 *********************** 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 109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.843 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 80 MET cc_start: 0.7373 (tmm) cc_final: 0.7081 (ttp) REVERT: A 229 PHE cc_start: 0.6367 (t80) cc_final: 0.5423 (t80) REVERT: B 139 MET cc_start: 0.8014 (mmt) cc_final: 0.7602 (tpp) REVERT: B 229 PHE cc_start: 0.7196 (t80) cc_final: 0.6883 (t80) REVERT: B 338 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8297 (mp10) outliers start: 21 outliers final: 12 residues processed: 107 average time/residue: 0.3179 time to fit residues: 45.1534 Evaluate side-chains 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 244 ARG 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 204 TYR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 378 HIS ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131405 restraints weight = 10530.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.135248 restraints weight = 8086.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136167 restraints weight = 6641.044| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7834 Z= 0.220 Angle : 0.682 10.338 10590 Z= 0.334 Chirality : 0.043 0.200 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.786 129.854 1042 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.72 % Favored : 92.86 % Rotamer: Outliers : 1.76 % Allowed : 27.82 % Favored : 70.42 % 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 (0.28), residues: 952 helix: 1.18 (0.23), residues: 490 sheet: -0.09 (0.50), residues: 95 loop : -1.81 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.014 0.001 HIS B 334 PHE 0.021 0.002 PHE A 373 TYR 0.033 0.002 TYR A 47 ARG 0.007 0.001 ARG A 151 *********************** 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 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.779 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: 0.6404 (t80) cc_final: 0.5486 (t80) REVERT: B 139 MET cc_start: 0.7925 (mmt) cc_final: 0.7557 (tpp) REVERT: B 229 PHE cc_start: 0.7132 (t80) cc_final: 0.6799 (t80) outliers start: 15 outliers final: 13 residues processed: 102 average time/residue: 0.3929 time to fit residues: 53.9776 Evaluate side-chains 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 316 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 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 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 = 0.4306 r_free = 0.4306 target = 0.180595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.145376 restraints weight = 10484.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149635 restraints weight = 16441.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.150919 restraints weight = 9799.242| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7834 Z= 0.203 Angle : 0.678 10.695 10590 Z= 0.331 Chirality : 0.042 0.166 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.599 131.261 1042 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.30 % Favored : 93.28 % Rotamer: Outliers : 1.64 % Allowed : 27.70 % 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: -0.02 (0.28), residues: 952 helix: 1.23 (0.23), residues: 490 sheet: 0.22 (0.50), residues: 97 loop : -1.87 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 114 HIS 0.014 0.001 HIS B 334 PHE 0.018 0.001 PHE A 373 TYR 0.027 0.002 TYR A 47 ARG 0.008 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 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.912 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: 0.6471 (t80) cc_final: 0.5594 (t80) REVERT: B 139 MET cc_start: 0.7936 (mmt) cc_final: 0.7645 (tpp) REVERT: B 229 PHE cc_start: 0.7200 (t80) cc_final: 0.6805 (t80) outliers start: 14 outliers final: 12 residues processed: 102 average time/residue: 0.2172 time to fit residues: 30.2403 Evaluate side-chains 97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU 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 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 316 VAL Chi-restraints excluded: chain B residue 322 ILE 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: 0.8980 chunk 86 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 22 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 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 = 0.4320 r_free = 0.4320 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.145581 restraints weight = 10558.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149919 restraints weight = 15033.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150695 restraints weight = 10654.943| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7834 Z= 0.198 Angle : 0.678 10.906 10590 Z= 0.331 Chirality : 0.043 0.207 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.517 131.290 1042 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.62 % Favored : 92.96 % Rotamer: Outliers : 2.00 % Allowed : 27.70 % 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: 0.02 (0.28), residues: 952 helix: 1.28 (0.23), residues: 487 sheet: 0.31 (0.49), residues: 97 loop : -1.88 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 114 HIS 0.006 0.001 HIS B 334 PHE 0.020 0.001 PHE A 373 TYR 0.026 0.002 TYR A 47 ARG 0.009 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 111 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 2.077 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: 0.6404 (t80) cc_final: 0.5542 (t80) REVERT: B 139 MET cc_start: 0.7922 (mmt) cc_final: 0.7635 (tpp) REVERT: B 229 PHE cc_start: 0.7177 (t80) cc_final: 0.6789 (t80) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.3399 time to fit residues: 50.9126 Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 271 SER Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 378 HIS 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: 0.1980 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.4332 r_free = 0.4332 target = 0.182215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135822 restraints weight = 10469.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.139135 restraints weight = 8845.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.139156 restraints weight = 6886.150| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7834 Z= 0.201 Angle : 0.692 10.871 10590 Z= 0.335 Chirality : 0.042 0.175 1182 Planarity : 0.004 0.049 1358 Dihedral : 8.511 131.889 1042 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 1.41 % Allowed : 28.40 % Favored : 70.19 % 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: 0.00 (0.27), residues: 952 helix: 1.28 (0.23), residues: 487 sheet: 0.36 (0.49), residues: 97 loop : -1.92 (0.33), residues: 368 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 0.027 0.002 PHE A 373 TYR 0.026 0.002 TYR A 47 ARG 0.009 0.001 ARG B 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.23 seconds wall clock time: 56 minutes 24.93 seconds (3384.93 seconds total)