Starting phenix.real_space_refine on Fri Dec 27 13:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcr_32428/12_2024/7wcr_32428.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.053 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3094 2.51 5 N 800 2.21 5 O 965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4880 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1563 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 4.40, per 1000 atoms: 0.90 Number of scatterers: 4880 At special positions: 0 Unit cell: (68.859, 87.44, 138.811, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 965 8.00 N 800 7.00 C 3094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.00 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 633.6 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 7.3% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.042A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.530A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.963A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.966A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.648A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 89 removed outlier: 3.826A pdb=" N LEU b 89 " --> pdb=" O ALA b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 132 Processing helix chain 'b' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.921A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'a' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLU a 10 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR a 33 " --> pdb=" O ASP a 99 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLU a 10 " --> pdb=" O THR a 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.735A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 124 through 128 removed outlier: 3.735A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.763A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL a 210 " --> pdb=" O VAL a 201 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR a 208 " --> pdb=" O HIS a 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.770A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP b 76 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 10 through 12 removed outlier: 7.079A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU b 39 " --> pdb=" O TYR b 55 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR b 55 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.732A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 121 through 123 removed outlier: 3.562A pdb=" N SER b 121 " --> pdb=" O PHE b 140 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL b 138 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU b 184 " --> pdb=" O VAL b 137 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS b 139 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER b 182 " --> pdb=" O CYS b 139 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.525A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR b 197 " --> pdb=" O PHE b 214 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE b 214 " --> pdb=" O TYR b 197 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS b 199 " --> pdb=" O LYS b 212 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS b 212 " --> pdb=" O CYS b 199 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA b 201 " --> pdb=" O ILE b 210 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE b 210 " --> pdb=" O ALA b 201 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 393 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: 1.42 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1398 1.33 - 1.46: 1043 1.46 - 1.58: 2540 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5007 Sorted by residual: bond pdb=" CA PHE A 490 " pdb=" C PHE A 490 " ideal model delta sigma weight residual 1.528 1.503 0.025 1.18e-02 7.18e+03 4.62e+00 bond pdb=" C ASN a 52 " pdb=" O ASN a 52 " ideal model delta sigma weight residual 1.241 1.213 0.027 1.33e-02 5.65e+03 4.22e+00 bond pdb=" CA GLN A 493 " pdb=" C GLN A 493 " ideal model delta sigma weight residual 1.528 1.497 0.031 1.51e-02 4.39e+03 4.11e+00 bond pdb=" CA ILE a 55 " pdb=" C ILE a 55 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.12e-02 7.97e+03 3.99e+00 bond pdb=" C LEU A 492 " pdb=" O LEU A 492 " ideal model delta sigma weight residual 1.235 1.214 0.021 1.18e-02 7.18e+03 3.18e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 6530 1.50 - 3.00: 240 3.00 - 4.51: 37 4.51 - 6.01: 8 6.01 - 7.51: 10 Bond angle restraints: 6825 Sorted by residual: angle pdb=" C LYS a 65 " pdb=" N ASP a 66 " pdb=" CA ASP a 66 " ideal model delta sigma weight residual 122.08 129.13 -7.05 1.47e+00 4.63e-01 2.30e+01 angle pdb=" N TYR A 489 " pdb=" CA TYR A 489 " pdb=" C TYR A 489 " ideal model delta sigma weight residual 109.65 116.18 -6.53 1.56e+00 4.11e-01 1.75e+01 angle pdb=" C ARG b 113 " pdb=" N ALA b 114 " pdb=" CA ALA b 114 " ideal model delta sigma weight residual 121.70 129.21 -7.51 1.80e+00 3.09e-01 1.74e+01 angle pdb=" N ASP a 56 " pdb=" CA ASP a 56 " pdb=" C ASP a 56 " ideal model delta sigma weight residual 111.39 117.09 -5.70 1.38e+00 5.25e-01 1.71e+01 angle pdb=" C ILE a 51 " pdb=" CA ILE a 51 " pdb=" CB ILE a 51 " ideal model delta sigma weight residual 111.29 105.20 6.09 1.64e+00 3.72e-01 1.38e+01 ... (remaining 6820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 2652 15.46 - 30.93: 244 30.93 - 46.39: 59 46.39 - 61.85: 14 61.85 - 77.31: 7 Dihedral angle restraints: 2976 sinusoidal: 1136 harmonic: 1840 Sorted by residual: dihedral pdb=" CB CYS b 139 " pdb=" SG CYS b 139 " pdb=" SG CYS b 199 " pdb=" CB CYS b 199 " ideal model delta sinusoidal sigma weight residual 93.00 169.59 -76.59 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 16.61 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 502 " pdb=" C GLY A 502 " pdb=" N VAL A 503 " pdb=" CA VAL A 503 " ideal model delta harmonic sigma weight residual -180.00 -138.94 -41.06 0 5.00e+00 4.00e-02 6.74e+01 ... (remaining 2973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 596 0.050 - 0.099: 118 0.099 - 0.149: 35 0.149 - 0.199: 5 0.199 - 0.248: 1 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA ASP a 56 " pdb=" N ASP a 56 " pdb=" C ASP a 56 " pdb=" CB ASP a 56 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE b 155 " pdb=" CA ILE b 155 " pdb=" CG1 ILE b 155 " pdb=" CG2 ILE b 155 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA TYR A 489 " pdb=" N TYR A 489 " pdb=" C TYR A 489 " pdb=" CB TYR A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 752 not shown) Planarity restraints: 875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 502 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLY A 502 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY A 502 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 503 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU a 152 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO a 153 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO a 153 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO a 153 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 491 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.025 5.00e-02 4.00e+02 ... (remaining 872 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 5 2.35 - 2.99: 2317 2.99 - 3.63: 6348 3.63 - 4.26: 10307 4.26 - 4.90: 17217 Nonbonded interactions: 36194 Sorted by model distance: nonbonded pdb=" CD1 LEU A 455 " pdb=" OE1 GLN A 493 " model vdw 1.713 3.460 nonbonded pdb=" CD1 LEU A 455 " pdb=" CD GLN A 493 " model vdw 1.960 3.690 nonbonded pdb=" CD1 LEU A 455 " pdb=" NE2 GLN A 493 " model vdw 2.206 3.540 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP b 88 " pdb=" OH TYR b 92 " model vdw 2.314 3.040 ... (remaining 36189 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 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 0.031 5007 Z= 0.197 Angle : 0.708 7.512 6825 Z= 0.420 Chirality : 0.046 0.248 755 Planarity : 0.006 0.046 875 Dihedral : 12.878 77.314 1776 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.73 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 5.65 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.76 (0.28), residues: 622 helix: -5.01 (0.15), residues: 42 sheet: -0.54 (0.32), residues: 223 loop : -2.37 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.011 0.001 PHE b 144 TYR 0.010 0.001 TYR A 501 ARG 0.001 0.000 ARG b 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.7911 (mp) cc_final: 0.7528 (pt) REVERT: b 42 TYR cc_start: 0.7893 (m-80) cc_final: 0.7493 (m-80) outliers start: 7 outliers final: 5 residues processed: 186 average time/residue: 0.1945 time to fit residues: 45.7117 Evaluate side-chains 140 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain a residue 52 ASN Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.0070 chunk 18 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 overall best weight: 0.3814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 GLN b 34 ASN b 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5007 Z= 0.193 Angle : 0.575 7.915 6825 Z= 0.297 Chirality : 0.043 0.175 755 Planarity : 0.005 0.056 875 Dihedral : 5.414 55.223 694 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.91 % Allowed : 14.21 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.30), residues: 622 helix: -4.25 (0.32), residues: 42 sheet: 0.01 (0.32), residues: 232 loop : -1.78 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 36 HIS 0.005 0.001 HIS b 203 PHE 0.015 0.001 PHE b 77 TYR 0.017 0.002 TYR a 179 ARG 0.006 0.001 ARG b 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.6464 (t0) cc_final: 0.6003 (m-40) REVERT: A 468 ILE cc_start: 0.8017 (mp) cc_final: 0.7798 (mp) REVERT: a 19 LYS cc_start: 0.7274 (mttt) cc_final: 0.6895 (pttm) REVERT: a 90 ASP cc_start: 0.7607 (m-30) cc_final: 0.7336 (m-30) REVERT: a 185 VAL cc_start: 0.7158 (m) cc_final: 0.6888 (t) REVERT: a 195 GLU cc_start: 0.6188 (tp30) cc_final: 0.5818 (mt-10) REVERT: b 4 MET cc_start: 0.6500 (mtt) cc_final: 0.6159 (mtt) REVERT: b 42 TYR cc_start: 0.8055 (m-80) cc_final: 0.7717 (m-80) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.1509 time to fit residues: 28.7329 Evaluate side-chains 134 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 183 SER Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 34 ASN Chi-restraints excluded: chain b residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.0030 chunk 18 optimal weight: 0.0770 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5007 Z= 0.172 Angle : 0.553 7.011 6825 Z= 0.284 Chirality : 0.043 0.189 755 Planarity : 0.004 0.047 875 Dihedral : 4.681 48.638 689 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.55 % Allowed : 16.39 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.32), residues: 622 helix: -3.48 (0.53), residues: 42 sheet: 0.34 (0.33), residues: 235 loop : -1.49 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS b 203 PHE 0.019 0.001 PHE b 77 TYR 0.017 0.002 TYR A 449 ARG 0.006 0.000 ARG b 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.4980 (m-80) cc_final: 0.4576 (m-10) REVERT: A 448 ASN cc_start: 0.6457 (t0) cc_final: 0.6202 (m-40) REVERT: A 468 ILE cc_start: 0.7995 (mp) cc_final: 0.7768 (mp) REVERT: a 19 LYS cc_start: 0.7219 (mttt) cc_final: 0.6843 (pttm) REVERT: a 90 ASP cc_start: 0.7454 (m-30) cc_final: 0.7111 (m-30) REVERT: b 42 TYR cc_start: 0.8137 (m-80) cc_final: 0.7795 (m-80) REVERT: b 147 LYS cc_start: 0.7144 (pttt) cc_final: 0.6936 (mtmt) REVERT: b 200 GLU cc_start: 0.7773 (tt0) cc_final: 0.7424 (tp30) outliers start: 14 outliers final: 13 residues processed: 135 average time/residue: 0.1571 time to fit residues: 27.3822 Evaluate side-chains 132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN b 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5007 Z= 0.154 Angle : 0.527 7.010 6825 Z= 0.270 Chirality : 0.042 0.164 755 Planarity : 0.004 0.045 875 Dihedral : 4.585 47.255 688 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.91 % Allowed : 17.30 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.99 (0.32), residues: 622 helix: -2.86 (0.75), residues: 36 sheet: 0.53 (0.33), residues: 238 loop : -1.31 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 36 HIS 0.001 0.000 HIS a 203 PHE 0.017 0.001 PHE b 77 TYR 0.017 0.001 TYR A 449 ARG 0.004 0.000 ARG b 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.5326 (m-80) cc_final: 0.4989 (m-10) REVERT: A 448 ASN cc_start: 0.6342 (t0) cc_final: 0.5728 (m-40) REVERT: A 468 ILE cc_start: 0.7923 (mp) cc_final: 0.7722 (mp) REVERT: a 19 LYS cc_start: 0.7246 (mttt) cc_final: 0.6927 (pttm) REVERT: a 90 ASP cc_start: 0.7516 (m-30) cc_final: 0.7133 (m-30) REVERT: b 42 TYR cc_start: 0.8147 (m-80) cc_final: 0.7848 (m-80) REVERT: b 200 GLU cc_start: 0.7887 (tt0) cc_final: 0.7602 (tp30) outliers start: 16 outliers final: 9 residues processed: 129 average time/residue: 0.1516 time to fit residues: 25.5255 Evaluate side-chains 122 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 5007 Z= 0.518 Angle : 0.813 9.486 6825 Z= 0.426 Chirality : 0.049 0.328 755 Planarity : 0.006 0.044 875 Dihedral : 6.403 57.392 688 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.28 % Allowed : 18.40 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.32), residues: 622 helix: -2.55 (0.89), residues: 30 sheet: 0.55 (0.33), residues: 225 loop : -1.52 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP b 153 HIS 0.005 0.001 HIS A 519 PHE 0.025 0.003 PHE a 104 TYR 0.026 0.003 TYR A 451 ARG 0.006 0.001 ARG a 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8272 (mp) cc_final: 0.7950 (mp) REVERT: A 495 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.7035 (t80) REVERT: a 19 LYS cc_start: 0.7504 (mttt) cc_final: 0.7295 (pttm) REVERT: a 90 ASP cc_start: 0.7757 (m-30) cc_final: 0.7393 (m-30) REVERT: a 109 GLN cc_start: 0.7414 (tm-30) cc_final: 0.7104 (tp40) REVERT: a 139 MET cc_start: 0.4785 (mmm) cc_final: 0.4456 (mtp) REVERT: b 52 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7030 (tp) REVERT: b 64 VAL cc_start: 0.7631 (t) cc_final: 0.7348 (t) REVERT: b 97 TYR cc_start: 0.3744 (OUTLIER) cc_final: 0.3057 (m-80) outliers start: 29 outliers final: 22 residues processed: 142 average time/residue: 0.1584 time to fit residues: 29.2678 Evaluate side-chains 139 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 ILE Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 97 TYR Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 142 ASN Chi-restraints excluded: chain b residue 175 ASP Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5007 Z= 0.222 Angle : 0.619 7.613 6825 Z= 0.319 Chirality : 0.044 0.168 755 Planarity : 0.004 0.041 875 Dihedral : 5.705 57.731 688 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.64 % Allowed : 21.49 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.91 (0.32), residues: 622 helix: -2.42 (0.94), residues: 30 sheet: 0.70 (0.33), residues: 224 loop : -1.35 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 153 HIS 0.005 0.001 HIS a 203 PHE 0.018 0.002 PHE b 77 TYR 0.020 0.002 TYR A 451 ARG 0.007 0.001 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.5907 (m-80) cc_final: 0.5697 (m-10) REVERT: A 451 TYR cc_start: 0.8081 (m-80) cc_final: 0.7871 (m-10) REVERT: A 458 LYS cc_start: 0.8479 (ptmt) cc_final: 0.7458 (mmtm) REVERT: A 468 ILE cc_start: 0.8159 (mp) cc_final: 0.7879 (mp) REVERT: A 495 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6776 (t80) REVERT: a 19 LYS cc_start: 0.7416 (mttt) cc_final: 0.7157 (pttm) REVERT: a 90 ASP cc_start: 0.7758 (m-30) cc_final: 0.7389 (m-30) REVERT: a 139 MET cc_start: 0.5415 (mmm) cc_final: 0.4874 (mtt) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.1610 time to fit residues: 27.9048 Evaluate side-chains 137 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 0.0870 chunk 35 optimal weight: 0.0060 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN b 34 ASN ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5007 Z= 0.176 Angle : 0.578 7.445 6825 Z= 0.295 Chirality : 0.044 0.165 755 Planarity : 0.004 0.038 875 Dihedral : 5.075 48.176 688 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.83 % Allowed : 21.86 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.75 (0.33), residues: 622 helix: -2.71 (0.81), residues: 36 sheet: 0.78 (0.32), residues: 235 loop : -1.20 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS a 203 PHE 0.018 0.001 PHE b 77 TYR 0.015 0.001 TYR A 451 ARG 0.003 0.000 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.5800 (m-80) cc_final: 0.5568 (m-10) REVERT: A 451 TYR cc_start: 0.7948 (m-80) cc_final: 0.7702 (m-10) REVERT: A 458 LYS cc_start: 0.8393 (ptmt) cc_final: 0.7504 (mmmt) REVERT: A 468 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 495 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6833 (t80) REVERT: a 19 LYS cc_start: 0.7369 (mttt) cc_final: 0.7099 (pttm) REVERT: a 90 ASP cc_start: 0.7738 (m-30) cc_final: 0.7363 (m-30) REVERT: a 139 MET cc_start: 0.5517 (mmm) cc_final: 0.4876 (mtt) REVERT: a 178 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6912 (mt) outliers start: 21 outliers final: 16 residues processed: 130 average time/residue: 0.1483 time to fit residues: 25.3669 Evaluate side-chains 132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0060 chunk 46 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 194 HIS ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5007 Z= 0.211 Angle : 0.593 7.543 6825 Z= 0.302 Chirality : 0.043 0.162 755 Planarity : 0.004 0.037 875 Dihedral : 4.972 47.567 688 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.64 % Allowed : 22.22 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.69 (0.33), residues: 622 helix: -2.71 (0.82), residues: 36 sheet: 1.00 (0.34), residues: 223 loop : -1.22 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 158 HIS 0.005 0.001 HIS a 203 PHE 0.017 0.001 PHE b 77 TYR 0.014 0.002 TYR A 451 ARG 0.002 0.000 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 TYR cc_start: 0.5939 (m-80) cc_final: 0.5663 (m-10) REVERT: A 451 TYR cc_start: 0.8041 (m-80) cc_final: 0.7764 (m-10) REVERT: A 458 LYS cc_start: 0.8372 (ptmt) cc_final: 0.7516 (mmmt) REVERT: A 468 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7818 (mp) REVERT: A 495 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6921 (t80) REVERT: a 19 LYS cc_start: 0.7433 (mttt) cc_final: 0.7125 (pttm) REVERT: a 90 ASP cc_start: 0.7764 (m-30) cc_final: 0.7397 (m-30) REVERT: a 139 MET cc_start: 0.5604 (mmm) cc_final: 0.4955 (mtt) REVERT: a 178 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6953 (mt) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.1553 time to fit residues: 24.7724 Evaluate side-chains 132 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.193 Angle : 0.585 8.011 6825 Z= 0.299 Chirality : 0.044 0.165 755 Planarity : 0.004 0.036 875 Dihedral : 4.795 47.520 686 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.28 % Allowed : 22.59 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.65 (0.33), residues: 622 helix: -2.41 (0.94), residues: 30 sheet: 1.00 (0.34), residues: 224 loop : -1.25 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 158 HIS 0.005 0.001 HIS a 203 PHE 0.017 0.001 PHE b 77 TYR 0.014 0.002 TYR A 451 ARG 0.002 0.000 ARG b 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6123 (m-80) cc_final: 0.5861 (m-10) REVERT: A 451 TYR cc_start: 0.8086 (m-80) cc_final: 0.7866 (m-10) REVERT: A 458 LYS cc_start: 0.8452 (ptmt) cc_final: 0.7558 (mmmt) REVERT: A 468 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 495 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6881 (t80) REVERT: a 19 LYS cc_start: 0.7461 (mttt) cc_final: 0.7154 (pttm) REVERT: a 41 HIS cc_start: 0.5090 (m-70) cc_final: 0.4850 (m-70) REVERT: a 90 ASP cc_start: 0.7763 (m-30) cc_final: 0.7385 (m-30) REVERT: a 139 MET cc_start: 0.5609 (mmm) cc_final: 0.5224 (mtt) REVERT: a 178 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6956 (mt) REVERT: b 4 MET cc_start: 0.6379 (mtt) cc_final: 0.6134 (mtt) outliers start: 18 outliers final: 15 residues processed: 134 average time/residue: 0.1511 time to fit residues: 26.6132 Evaluate side-chains 135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS a 200 ASN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5007 Z= 0.216 Angle : 0.608 8.676 6825 Z= 0.310 Chirality : 0.044 0.169 755 Planarity : 0.004 0.036 875 Dihedral : 4.845 47.391 686 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.19 % Allowed : 22.59 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.62 (0.33), residues: 622 helix: -2.50 (0.92), residues: 30 sheet: 1.02 (0.34), residues: 224 loop : -1.21 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 158 HIS 0.006 0.001 HIS a 203 PHE 0.017 0.001 PHE b 77 TYR 0.013 0.002 TYR A 451 ARG 0.002 0.000 ARG b 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 380 TYR cc_start: 0.6195 (m-80) cc_final: 0.5939 (m-10) REVERT: A 451 TYR cc_start: 0.8133 (m-80) cc_final: 0.7850 (m-10) REVERT: A 458 LYS cc_start: 0.8483 (ptmt) cc_final: 0.7524 (mmmt) REVERT: A 468 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 495 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6733 (t80) REVERT: a 19 LYS cc_start: 0.7533 (mttt) cc_final: 0.7178 (pttm) REVERT: a 90 ASP cc_start: 0.7795 (m-30) cc_final: 0.7413 (m-30) REVERT: a 139 MET cc_start: 0.5658 (mmm) cc_final: 0.5311 (mtt) REVERT: a 178 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6994 (mt) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.1866 time to fit residues: 33.0965 Evaluate side-chains 138 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 HIS ** 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 = 0.4296 r_free = 0.4296 target = 0.193290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.172622 restraints weight = 8588.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176578 restraints weight = 5187.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179248 restraints weight = 3576.495| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5007 Z= 0.210 Angle : 0.608 8.296 6825 Z= 0.309 Chirality : 0.044 0.168 755 Planarity : 0.004 0.035 875 Dihedral : 4.912 47.904 686 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.28 % Allowed : 24.04 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % 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: -0.61 (0.33), residues: 622 helix: -2.50 (0.92), residues: 30 sheet: 1.03 (0.34), residues: 225 loop : -1.22 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP a 158 HIS 0.006 0.001 HIS a 203 PHE 0.016 0.001 PHE b 77 TYR 0.014 0.002 TYR A 451 ARG 0.002 0.000 ARG b 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1735.25 seconds wall clock time: 32 minutes 42.63 seconds (1962.63 seconds total)