Starting phenix.real_space_refine on Thu Jun 5 02:46:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcr_32428/06_2025/7wcr_32428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcr_32428/06_2025/7wcr_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_32428/06_2025/7wcr_32428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcr_32428/06_2025/7wcr_32428.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcr_32428/06_2025/7wcr_32428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcr_32428/06_2025/7wcr_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-5710/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: 4.12, per 1000 atoms: 0.84 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: 0.98 Conformation dependent library (CDL) restraints added in 554.4 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: 0.60 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: 1.27 Time building geometry restraints manager: 1.22 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: 5.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.620 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:2.740 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- 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 5015 Z= 0.188 Angle : 0.707 7.512 6841 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 Details of bonding type rmsd hydrogen bonds : bond 0.29167 ( 143) hydrogen bonds : angle 10.67775 ( 393) SS BOND : bond 0.01092 ( 8) SS BOND : angle 0.53015 ( 16) covalent geometry : bond 0.00311 ( 5007) covalent geometry : angle 0.70769 ( 6825) *********************** 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 : 0.499 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: 0.1691 time to fit residues: 39.6405 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 : 0.556 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.207229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.184760 restraints weight = 8415.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.189403 restraints weight = 4877.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.192597 restraints weight = 3242.713| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 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 5015 Z= 0.129 Angle : 0.575 7.915 6841 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 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 143) hydrogen bonds : angle 7.21078 ( 393) SS BOND : bond 0.00357 ( 8) SS BOND : angle 0.56222 ( 16) covalent geometry : bond 0.00287 ( 5007) covalent geometry : angle 0.57457 ( 6825) *********************** 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 : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8059 (p90) cc_final: 0.7788 (p90) REVERT: A 448 ASN cc_start: 0.6582 (t0) cc_final: 0.6077 (m-40) REVERT: A 468 ILE cc_start: 0.7996 (mp) cc_final: 0.7766 (mp) REVERT: a 10 GLU cc_start: 0.7229 (mp0) cc_final: 0.7020 (mp0) REVERT: a 19 LYS cc_start: 0.7457 (mttt) cc_final: 0.6960 (pttm) REVERT: a 90 ASP cc_start: 0.7577 (m-30) cc_final: 0.7297 (m-30) REVERT: a 185 VAL cc_start: 0.7243 (m) cc_final: 0.6941 (t) REVERT: a 195 GLU cc_start: 0.6296 (tp30) cc_final: 0.5825 (mt-10) REVERT: b 4 MET cc_start: 0.6585 (mtt) cc_final: 0.6193 (mtt) REVERT: b 42 TYR cc_start: 0.8101 (m-80) cc_final: 0.7716 (m-80) REVERT: b 147 LYS cc_start: 0.7167 (pttt) cc_final: 0.6959 (pttt) REVERT: b 210 ILE cc_start: 0.7702 (mt) cc_final: 0.7492 (pt) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.1394 time to fit residues: 26.7129 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 : 0.494 ------------------------------------------------------------------------------- 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 35 optimal weight: 0.0170 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 GLN a 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.198159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.175972 restraints weight = 8455.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.180260 restraints weight = 5018.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183217 restraints weight = 3424.265| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5015 Z= 0.194 Angle : 0.624 6.751 6841 Z= 0.326 Chirality : 0.045 0.185 755 Planarity : 0.005 0.048 875 Dihedral : 5.167 48.781 689 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.46 % Allowed : 17.30 % Favored : 79.23 % 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: -1.30 (0.32), residues: 622 helix: -3.29 (0.64), residues: 36 sheet: 0.31 (0.33), residues: 238 loop : -1.49 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 153 HIS 0.004 0.001 HIS b 203 PHE 0.023 0.002 PHE b 77 TYR 0.019 0.002 TYR A 453 ARG 0.006 0.001 ARG b 60 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 143) hydrogen bonds : angle 6.19841 ( 393) SS BOND : bond 0.00481 ( 8) SS BOND : angle 0.71222 ( 16) covalent geometry : bond 0.00438 ( 5007) covalent geometry : angle 0.62382 ( 6825) *********************** 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 151 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8134 (p90) cc_final: 0.7859 (p90) REVERT: A 468 ILE cc_start: 0.8085 (mp) cc_final: 0.7835 (mp) REVERT: a 19 LYS cc_start: 0.7585 (mttt) cc_final: 0.7121 (pttm) REVERT: a 90 ASP cc_start: 0.7612 (m-30) cc_final: 0.7209 (m-30) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.1546 time to fit residues: 28.2536 Evaluate side-chains 131 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 407 VAL Chi-restraints excluded: chain A residue 489 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 128 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 175 ASP 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 19 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN b 34 ASN b 44 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.199648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.177562 restraints weight = 8484.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181866 restraints weight = 5053.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.184949 restraints weight = 3447.159| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5015 Z= 0.122 Angle : 0.557 7.153 6841 Z= 0.288 Chirality : 0.043 0.180 755 Planarity : 0.004 0.045 875 Dihedral : 4.883 48.659 688 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.28 % Allowed : 19.13 % Favored : 77.60 % 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: -1.07 (0.32), residues: 622 helix: -2.71 (0.78), residues: 36 sheet: 0.51 (0.33), residues: 238 loop : -1.41 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.005 0.001 HIS a 203 PHE 0.019 0.002 PHE b 77 TYR 0.016 0.001 TYR b 55 ARG 0.003 0.000 ARG b 113 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 143) hydrogen bonds : angle 5.68629 ( 393) SS BOND : bond 0.00357 ( 8) SS BOND : angle 0.70267 ( 16) covalent geometry : bond 0.00274 ( 5007) covalent geometry : angle 0.55627 ( 6825) *********************** 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 139 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8207 (p90) cc_final: 0.7941 (p90) REVERT: A 455 LEU cc_start: 0.6905 (mp) cc_final: 0.6279 (mp) REVERT: A 468 ILE cc_start: 0.8012 (mp) cc_final: 0.7738 (mp) REVERT: a 19 LYS cc_start: 0.7535 (mttt) cc_final: 0.7094 (pttm) REVERT: a 90 ASP cc_start: 0.7656 (m-30) cc_final: 0.7223 (m-30) REVERT: a 139 MET cc_start: 0.4951 (mmm) cc_final: 0.4269 (mtp) REVERT: a 154 VAL cc_start: 0.6726 (m) cc_final: 0.6325 (m) REVERT: b 42 TYR cc_start: 0.8151 (m-80) cc_final: 0.7809 (m-80) REVERT: b 97 TYR cc_start: 0.3108 (OUTLIER) cc_final: 0.1873 (m-80) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 0.1422 time to fit residues: 24.4739 Evaluate side-chains 129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 489 TYR 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 160 SER Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain b residue 19 VAL 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 119 THR Chi-restraints excluded: chain b residue 197 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.197491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.175968 restraints weight = 8802.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180371 restraints weight = 5147.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183298 restraints weight = 3450.974| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5015 Z= 0.147 Angle : 0.583 8.869 6841 Z= 0.300 Chirality : 0.043 0.170 755 Planarity : 0.004 0.044 875 Dihedral : 5.053 47.269 688 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.19 % Allowed : 18.76 % Favored : 77.05 % 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: -0.86 (0.33), residues: 622 helix: -2.61 (0.74), residues: 42 sheet: 0.70 (0.33), residues: 236 loop : -1.26 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 192 HIS 0.002 0.001 HIS a 168 PHE 0.018 0.002 PHE b 77 TYR 0.012 0.002 TYR A 449 ARG 0.002 0.000 ARG b 113 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 143) hydrogen bonds : angle 5.54098 ( 393) SS BOND : bond 0.00403 ( 8) SS BOND : angle 0.74273 ( 16) covalent geometry : bond 0.00332 ( 5007) covalent geometry : angle 0.58306 ( 6825) *********************** 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 143 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8251 (p90) cc_final: 0.7923 (p90) REVERT: A 468 ILE cc_start: 0.8084 (mp) cc_final: 0.7835 (mp) REVERT: A 474 GLN cc_start: 0.7057 (mt0) cc_final: 0.6780 (mt0) REVERT: a 19 LYS cc_start: 0.7555 (mttt) cc_final: 0.7111 (pttm) REVERT: a 90 ASP cc_start: 0.7838 (m-30) cc_final: 0.7430 (m-30) REVERT: b 42 TYR cc_start: 0.8154 (m-80) cc_final: 0.7886 (m-80) REVERT: b 97 TYR cc_start: 0.3293 (OUTLIER) cc_final: 0.2286 (m-80) outliers start: 23 outliers final: 17 residues processed: 132 average time/residue: 0.1578 time to fit residues: 26.9165 Evaluate side-chains 129 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 489 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 160 SER Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain b residue 19 VAL Chi-restraints excluded: chain b residue 60 ARG 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 119 THR 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 34 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS b 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170318 restraints weight = 8680.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174537 restraints weight = 5123.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177420 restraints weight = 3486.542| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 5015 Z= 0.209 Angle : 0.644 7.088 6841 Z= 0.337 Chirality : 0.045 0.171 755 Planarity : 0.005 0.041 875 Dihedral : 5.600 53.721 688 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.19 % Allowed : 19.85 % Favored : 75.96 % 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: -0.68 (0.33), residues: 622 helix: -1.57 (1.14), residues: 24 sheet: 0.85 (0.34), residues: 224 loop : -1.27 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a 158 HIS 0.004 0.001 HIS a 203 PHE 0.020 0.002 PHE b 77 TYR 0.019 0.002 TYR A 421 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 143) hydrogen bonds : angle 5.73530 ( 393) SS BOND : bond 0.00462 ( 8) SS BOND : angle 0.93864 ( 16) covalent geometry : bond 0.00484 ( 5007) covalent geometry : angle 0.64291 ( 6825) *********************** 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 145 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8275 (p90) cc_final: 0.7943 (p90) REVERT: A 458 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7238 (mmtm) REVERT: A 468 ILE cc_start: 0.8127 (mp) cc_final: 0.7830 (mp) REVERT: A 474 GLN cc_start: 0.7126 (mt0) cc_final: 0.6773 (mt0) REVERT: a 19 LYS cc_start: 0.7545 (mttt) cc_final: 0.7193 (pttm) REVERT: a 90 ASP cc_start: 0.7739 (m-30) cc_final: 0.7358 (m-30) REVERT: a 139 MET cc_start: 0.5066 (mmm) cc_final: 0.4596 (mtt) REVERT: b 97 TYR cc_start: 0.3608 (OUTLIER) cc_final: 0.2569 (m-80) REVERT: b 180 MET cc_start: 0.7248 (ttt) cc_final: 0.7040 (ttm) outliers start: 23 outliers final: 20 residues processed: 133 average time/residue: 0.1703 time to fit residues: 30.0558 Evaluate side-chains 136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain a residue 28 THR 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 97 TYR Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 149 ILE 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 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.193937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173005 restraints weight = 8673.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.177098 restraints weight = 5198.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179888 restraints weight = 3539.205| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5015 Z= 0.141 Angle : 0.587 7.834 6841 Z= 0.304 Chirality : 0.044 0.163 755 Planarity : 0.004 0.040 875 Dihedral : 5.432 57.812 688 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.01 % Allowed : 20.58 % Favored : 75.41 % 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: -0.66 (0.34), residues: 622 helix: -2.31 (0.97), residues: 30 sheet: 0.88 (0.34), residues: 224 loop : -1.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 158 HIS 0.002 0.000 HIS a 203 PHE 0.018 0.001 PHE b 77 TYR 0.010 0.002 TYR A 449 ARG 0.002 0.000 ARG b 60 Details of bonding type rmsd hydrogen bonds : bond 0.03008 ( 143) hydrogen bonds : angle 5.50510 ( 393) SS BOND : bond 0.00385 ( 8) SS BOND : angle 0.89291 ( 16) covalent geometry : bond 0.00319 ( 5007) covalent geometry : angle 0.58632 ( 6825) *********************** 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: 22 poor density : 118 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8228 (p90) cc_final: 0.7926 (p90) REVERT: A 458 LYS cc_start: 0.8297 (ptmt) cc_final: 0.7328 (mmmt) REVERT: A 468 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 474 GLN cc_start: 0.7206 (mt0) cc_final: 0.6930 (mt0) REVERT: a 19 LYS cc_start: 0.7402 (mttt) cc_final: 0.7113 (pttm) REVERT: a 90 ASP cc_start: 0.7726 (m-30) cc_final: 0.7372 (m-30) REVERT: a 139 MET cc_start: 0.5480 (mmm) cc_final: 0.5028 (mtt) REVERT: a 178 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6949 (mt) REVERT: b 97 TYR cc_start: 0.3831 (OUTLIER) cc_final: 0.2441 (m-80) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.1566 time to fit residues: 26.3285 Evaluate side-chains 134 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 468 ILE 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 11 LEU 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 210 VAL Chi-restraints excluded: chain b residue 19 VAL 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 197 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.193310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172254 restraints weight = 8674.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.176246 restraints weight = 5234.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.178995 restraints weight = 3615.444| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5015 Z= 0.149 Angle : 0.594 8.654 6841 Z= 0.309 Chirality : 0.044 0.170 755 Planarity : 0.004 0.037 875 Dihedral : 5.212 47.311 688 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.19 % Allowed : 20.58 % Favored : 75.23 % 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: -0.58 (0.34), residues: 622 helix: -2.33 (0.97), residues: 30 sheet: 0.98 (0.34), residues: 224 loop : -1.14 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 158 HIS 0.005 0.001 HIS a 203 PHE 0.017 0.001 PHE b 77 TYR 0.010 0.002 TYR a 126 ARG 0.002 0.000 ARG b 160 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 143) hydrogen bonds : angle 5.35934 ( 393) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.86849 ( 16) covalent geometry : bond 0.00338 ( 5007) covalent geometry : angle 0.59310 ( 6825) *********************** 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 136 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8240 (p90) cc_final: 0.7930 (p90) REVERT: A 458 LYS cc_start: 0.8316 (ptmt) cc_final: 0.7416 (mmmt) REVERT: A 468 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7795 (mp) REVERT: A 474 GLN cc_start: 0.7261 (mt0) cc_final: 0.6979 (mt0) REVERT: a 19 LYS cc_start: 0.7492 (mttt) cc_final: 0.7169 (pttm) REVERT: a 41 HIS cc_start: 0.5085 (OUTLIER) cc_final: 0.4821 (m-70) REVERT: a 90 ASP cc_start: 0.7752 (m-30) cc_final: 0.7404 (m-30) REVERT: a 139 MET cc_start: 0.5487 (mmm) cc_final: 0.5044 (mtt) REVERT: a 178 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6947 (mt) REVERT: b 97 TYR cc_start: 0.3915 (OUTLIER) cc_final: 0.2525 (m-80) outliers start: 23 outliers final: 17 residues processed: 123 average time/residue: 0.1654 time to fit residues: 26.4492 Evaluate side-chains 134 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 468 ILE 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 11 LEU 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 210 VAL Chi-restraints excluded: chain b residue 19 VAL 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 149 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS a 62 GLN a 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.170606 restraints weight = 8619.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174477 restraints weight = 5307.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.177240 restraints weight = 3720.694| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5015 Z= 0.197 Angle : 0.656 9.538 6841 Z= 0.342 Chirality : 0.045 0.168 755 Planarity : 0.005 0.041 875 Dihedral : 5.435 47.031 688 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.37 % Allowed : 21.13 % Favored : 74.50 % 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: -0.72 (0.33), residues: 622 helix: -2.43 (0.95), residues: 30 sheet: 0.93 (0.34), residues: 219 loop : -1.24 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 153 HIS 0.002 0.001 HIS A 519 PHE 0.018 0.002 PHE b 77 TYR 0.017 0.002 TYR A 380 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 143) hydrogen bonds : angle 5.63362 ( 393) SS BOND : bond 0.00459 ( 8) SS BOND : angle 1.20731 ( 16) covalent geometry : bond 0.00453 ( 5007) covalent geometry : angle 0.65444 ( 6825) *********************** 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 144 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8251 (p90) cc_final: 0.7946 (p90) REVERT: A 380 TYR cc_start: 0.6556 (m-80) cc_final: 0.6220 (m-10) REVERT: A 458 LYS cc_start: 0.8415 (ptmt) cc_final: 0.7458 (mmmt) REVERT: A 468 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7844 (mp) REVERT: A 474 GLN cc_start: 0.7358 (mt0) cc_final: 0.7041 (mt0) REVERT: A 495 TYR cc_start: 0.6954 (t80) cc_final: 0.6681 (t80) REVERT: a 19 LYS cc_start: 0.7584 (mttt) cc_final: 0.7272 (pttm) REVERT: a 41 HIS cc_start: 0.5215 (OUTLIER) cc_final: 0.4961 (m170) REVERT: a 90 ASP cc_start: 0.7821 (m-30) cc_final: 0.7462 (m-30) REVERT: a 178 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6925 (mt) REVERT: b 97 TYR cc_start: 0.3656 (OUTLIER) cc_final: 0.2955 (m-80) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 0.1496 time to fit residues: 25.7486 Evaluate side-chains 137 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS 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 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 41 HIS Chi-restraints excluded: chain a residue 178 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 84 VAL Chi-restraints excluded: chain b residue 97 TYR Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 149 ILE 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 46 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.193053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.172274 restraints weight = 8749.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176220 restraints weight = 5326.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178891 restraints weight = 3702.620| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5015 Z= 0.149 Angle : 0.608 8.913 6841 Z= 0.316 Chirality : 0.044 0.172 755 Planarity : 0.004 0.041 875 Dihedral : 5.128 47.786 686 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.01 % Allowed : 21.49 % Favored : 74.50 % 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: -0.67 (0.34), residues: 622 helix: -2.44 (0.95), residues: 30 sheet: 0.88 (0.34), residues: 224 loop : -1.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS a 203 PHE 0.016 0.001 PHE b 77 TYR 0.017 0.002 TYR A 451 ARG 0.002 0.000 ARG b 113 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 143) hydrogen bonds : angle 5.43874 ( 393) SS BOND : bond 0.00398 ( 8) SS BOND : angle 1.20212 ( 16) covalent geometry : bond 0.00341 ( 5007) covalent geometry : angle 0.60612 ( 6825) ********************** 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 143 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8224 (p90) cc_final: 0.7931 (p90) REVERT: A 380 TYR cc_start: 0.6453 (m-80) cc_final: 0.6220 (m-10) REVERT: A 451 TYR cc_start: 0.8161 (m-80) cc_final: 0.7831 (m-10) REVERT: A 458 LYS cc_start: 0.8492 (ptmt) cc_final: 0.7546 (mmmt) REVERT: A 468 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 474 GLN cc_start: 0.7291 (mt0) cc_final: 0.6985 (mt0) REVERT: a 19 LYS cc_start: 0.7581 (mttt) cc_final: 0.7279 (pttm) REVERT: a 178 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6913 (mt) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 0.1618 time to fit residues: 27.7513 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 : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS 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 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 178 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 84 VAL Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 149 ILE 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 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN a 168 HIS ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.191699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170847 restraints weight = 8748.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174757 restraints weight = 5350.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.177365 restraints weight = 3718.978| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5015 Z= 0.171 Angle : 0.635 10.679 6841 Z= 0.330 Chirality : 0.044 0.159 755 Planarity : 0.004 0.041 875 Dihedral : 5.248 47.297 686 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.46 % Allowed : 23.32 % 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: -0.72 (0.34), residues: 622 helix: -2.33 (1.00), residues: 30 sheet: 0.97 (0.34), residues: 220 loop : -1.29 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 158 HIS 0.003 0.001 HIS a 203 PHE 0.017 0.002 PHE b 77 TYR 0.020 0.002 TYR A 451 ARG 0.002 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 143) hydrogen bonds : angle 5.49355 ( 393) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.11957 ( 16) covalent geometry : bond 0.00393 ( 5007) covalent geometry : angle 0.63300 ( 6825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.10 seconds wall clock time: 48 minutes 3.88 seconds (2883.88 seconds total)