Starting phenix.real_space_refine on Tue Feb 3 16:19:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcr_32428/02_2026/7wcr_32428.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcr_32428/02_2026/7wcr_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_32428/02_2026/7wcr_32428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2026/7wcr_32428.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2026/7wcr_32428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcr_32428/02_2026/7wcr_32428.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 1.30, per 1000 atoms: 0.27 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: 0.53 Conformation dependent library (CDL) restraints added in 450.0 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: 0.20 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: 0.84 Time building geometry restraints manager: 0.73 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: 6.950 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.800 Find NCS groups from input model: 0.030 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG b 18 TYR 0.010 0.001 TYR A 501 PHE 0.011 0.001 PHE b 144 TRP 0.004 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5007) covalent geometry : angle 0.70769 ( 6825) SS BOND : bond 0.01092 ( 8) SS BOND : angle 0.53015 ( 16) hydrogen bonds : bond 0.29167 ( 143) hydrogen bonds : angle 10.67775 ( 393) *********************** 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 : 0.196 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: 0.0543 time to fit residues: 12.9908 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 : 0.105 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.0020 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 overall best weight: 0.3186 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.207115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.184700 restraints weight = 8459.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.189443 restraints weight = 4845.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.192641 restraints weight = 3193.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.194789 restraints weight = 2304.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196354 restraints weight = 1780.277| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5015 Z= 0.123 Angle : 0.574 7.869 6841 Z= 0.296 Chirality : 0.043 0.174 755 Planarity : 0.005 0.055 875 Dihedral : 5.365 55.518 694 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.30), residues: 622 helix: -4.25 (0.33), residues: 42 sheet: 0.01 (0.32), residues: 232 loop : -1.79 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 113 TYR 0.015 0.002 TYR b 55 PHE 0.015 0.001 PHE b 77 TRP 0.007 0.001 TRP a 36 HIS 0.008 0.001 HIS b 203 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5007) covalent geometry : angle 0.57393 ( 6825) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.54794 ( 16) hydrogen bonds : bond 0.04032 ( 143) hydrogen bonds : angle 7.18609 ( 393) *********************** 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 156 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8070 (p90) cc_final: 0.7796 (p90) REVERT: A 448 ASN cc_start: 0.6531 (t0) cc_final: 0.6160 (m-40) REVERT: A 468 ILE cc_start: 0.7970 (mp) cc_final: 0.7738 (mp) REVERT: a 10 GLU cc_start: 0.7259 (mp0) cc_final: 0.7026 (mp0) REVERT: a 19 LYS cc_start: 0.7412 (mttt) cc_final: 0.6913 (pttm) REVERT: a 90 ASP cc_start: 0.7594 (m-30) cc_final: 0.7289 (m-30) REVERT: a 185 VAL cc_start: 0.7290 (m) cc_final: 0.6977 (t) REVERT: a 195 GLU cc_start: 0.6174 (tp30) cc_final: 0.5819 (mt-10) REVERT: b 42 TYR cc_start: 0.8056 (m-80) cc_final: 0.7644 (m-80) REVERT: b 147 LYS cc_start: 0.7098 (pttt) cc_final: 0.6894 (pttt) REVERT: b 210 ILE cc_start: 0.7556 (mt) cc_final: 0.7355 (pt) outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 0.0458 time to fit residues: 8.8969 Evaluate side-chains 130 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 6 GLN a 43 GLN a 62 GLN b 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.204026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.181940 restraints weight = 8492.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.186523 restraints weight = 4970.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.189688 restraints weight = 3297.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.191577 restraints weight = 2392.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193190 restraints weight = 1883.111| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3136 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= 0.125 Angle : 0.552 6.666 6841 Z= 0.283 Chirality : 0.043 0.180 755 Planarity : 0.004 0.048 875 Dihedral : 4.711 48.753 689 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 15.85 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.32), residues: 622 helix: -3.45 (0.54), residues: 42 sheet: 0.38 (0.33), residues: 240 loop : -1.51 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 113 TYR 0.016 0.002 TYR A 449 PHE 0.020 0.001 PHE b 77 TRP 0.006 0.001 TRP a 36 HIS 0.003 0.001 HIS b 203 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 5007) covalent geometry : angle 0.55170 ( 6825) SS BOND : bond 0.00434 ( 8) SS BOND : angle 0.55598 ( 16) hydrogen bonds : bond 0.03273 ( 143) hydrogen bonds : angle 6.09954 ( 393) *********************** 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 133 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8050 (p90) cc_final: 0.7810 (p90) REVERT: A 380 TYR cc_start: 0.5061 (m-80) cc_final: 0.4608 (m-10) REVERT: A 448 ASN cc_start: 0.6561 (t0) cc_final: 0.6254 (m-40) REVERT: A 468 ILE cc_start: 0.8019 (mp) cc_final: 0.7764 (mp) REVERT: a 19 LYS cc_start: 0.7305 (mttt) cc_final: 0.6875 (pttm) REVERT: a 90 ASP cc_start: 0.7502 (m-30) cc_final: 0.7111 (m-30) REVERT: a 195 GLU cc_start: 0.6230 (tp30) cc_final: 0.6008 (mt-10) REVERT: b 42 TYR cc_start: 0.8224 (m-80) cc_final: 0.7874 (m-80) REVERT: b 200 GLU cc_start: 0.7871 (tt0) cc_final: 0.7573 (tp30) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.0471 time to fit residues: 7.8664 Evaluate side-chains 123 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain a residue 55 ILE Chi-restraints excluded: chain a residue 128 LEU 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 197 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN a 168 HIS b 34 ASN b 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.174265 restraints weight = 8380.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178523 restraints weight = 4979.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.181500 restraints weight = 3388.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.183461 restraints weight = 2507.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.185025 restraints weight = 1996.651| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.4127 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= 0.182 Angle : 0.628 6.845 6841 Z= 0.328 Chirality : 0.044 0.170 755 Planarity : 0.005 0.045 875 Dihedral : 5.385 47.739 688 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.01 % Allowed : 16.94 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.32), residues: 622 helix: -2.18 (0.90), residues: 30 sheet: 0.52 (0.32), residues: 238 loop : -1.39 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 113 TYR 0.019 0.002 TYR b 97 PHE 0.021 0.002 PHE b 77 TRP 0.013 0.001 TRP b 153 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5007) covalent geometry : angle 0.62704 ( 6825) SS BOND : bond 0.00463 ( 8) SS BOND : angle 0.84282 ( 16) hydrogen bonds : bond 0.03507 ( 143) hydrogen bonds : angle 5.78622 ( 393) *********************** 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 152 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8231 (p90) cc_final: 0.7942 (p90) REVERT: A 455 LEU cc_start: 0.6821 (mt) cc_final: 0.6395 (mp) REVERT: A 468 ILE cc_start: 0.8118 (mp) cc_final: 0.7846 (mp) REVERT: a 19 LYS cc_start: 0.7483 (mttt) cc_final: 0.7107 (pttm) REVERT: a 90 ASP cc_start: 0.7827 (m-30) cc_final: 0.7410 (m-30) REVERT: a 139 MET cc_start: 0.5105 (mmm) cc_final: 0.4563 (mtp) REVERT: b 42 TYR cc_start: 0.8220 (m-80) cc_final: 0.7949 (m-80) REVERT: b 97 TYR cc_start: 0.3044 (OUTLIER) cc_final: 0.2443 (m-80) REVERT: b 180 MET cc_start: 0.7230 (ttt) cc_final: 0.7000 (ttm) outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.0497 time to fit residues: 9.1264 Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 489 TYR Chi-restraints excluded: chain A residue 500 THR 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 84 VAL Chi-restraints excluded: chain b residue 97 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 62 GLN ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.195177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.173767 restraints weight = 8720.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177885 restraints weight = 5225.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.180734 restraints weight = 3593.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.182750 restraints weight = 2686.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184188 restraints weight = 2130.207| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5015 Z= 0.158 Angle : 0.618 8.708 6841 Z= 0.315 Chirality : 0.043 0.169 755 Planarity : 0.004 0.041 875 Dihedral : 5.302 49.192 688 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.64 % Allowed : 19.49 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.33), residues: 622 helix: -2.37 (0.93), residues: 30 sheet: 0.64 (0.33), residues: 238 loop : -1.24 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 113 TYR 0.013 0.002 TYR A 449 PHE 0.019 0.002 PHE b 77 TRP 0.008 0.001 TRP b 153 HIS 0.002 0.000 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 5007) covalent geometry : angle 0.61711 ( 6825) SS BOND : bond 0.00391 ( 8) SS BOND : angle 0.79881 ( 16) hydrogen bonds : bond 0.03131 ( 143) hydrogen bonds : angle 5.61908 ( 393) *********************** 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 138 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8163 (mp) cc_final: 0.7872 (mp) REVERT: a 19 LYS cc_start: 0.7245 (mttt) cc_final: 0.7036 (pttm) REVERT: a 90 ASP cc_start: 0.7807 (m-30) cc_final: 0.7430 (m-30) REVERT: a 139 MET cc_start: 0.5205 (mmm) cc_final: 0.4695 (mtm) REVERT: b 42 TYR cc_start: 0.8144 (m-80) cc_final: 0.7929 (m-80) outliers start: 20 outliers final: 15 residues processed: 130 average time/residue: 0.0622 time to fit residues: 10.4623 Evaluate side-chains 128 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 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 112 LEU Chi-restraints excluded: chain b residue 119 THR 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 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.0050 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 0.0670 chunk 25 optimal weight: 0.9980 overall best weight: 0.4732 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.196140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174779 restraints weight = 8756.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.179008 restraints weight = 5196.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181809 restraints weight = 3545.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.183714 restraints weight = 2647.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.185219 restraints weight = 2112.754| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4667 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= 0.131 Angle : 0.583 6.700 6841 Z= 0.302 Chirality : 0.044 0.171 755 Planarity : 0.004 0.040 875 Dihedral : 5.239 52.766 688 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.46 % Allowed : 20.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.33), residues: 622 helix: -2.34 (0.93), residues: 30 sheet: 0.72 (0.33), residues: 238 loop : -1.16 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 113 TYR 0.012 0.001 TYR A 449 PHE 0.018 0.001 PHE b 77 TRP 0.016 0.001 TRP a 158 HIS 0.002 0.000 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5007) covalent geometry : angle 0.58287 ( 6825) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.75731 ( 16) hydrogen bonds : bond 0.02835 ( 143) hydrogen bonds : angle 5.48068 ( 393) *********************** 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 134 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8266 (p90) cc_final: 0.8001 (p90) REVERT: A 458 LYS cc_start: 0.8120 (ptmt) cc_final: 0.7139 (mmmt) REVERT: A 468 ILE cc_start: 0.8107 (mp) cc_final: 0.7824 (mp) REVERT: A 474 GLN cc_start: 0.7012 (mt0) cc_final: 0.6775 (mt0) REVERT: a 19 LYS cc_start: 0.7294 (mttt) cc_final: 0.7015 (pttm) REVERT: a 90 ASP cc_start: 0.7694 (m-30) cc_final: 0.7309 (m-30) REVERT: a 139 MET cc_start: 0.5260 (mmm) cc_final: 0.4789 (mtm) REVERT: b 42 TYR cc_start: 0.8134 (m-80) cc_final: 0.7923 (m-80) REVERT: b 210 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7899 (tp) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 0.0550 time to fit residues: 8.9232 Evaluate side-chains 124 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 493 GLN 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 60 ARG Chi-restraints excluded: chain b residue 112 LEU Chi-restraints excluded: chain b residue 119 THR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 18 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 = 0.4315 r_free = 0.4315 target = 0.194753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.173384 restraints weight = 8702.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.177630 restraints weight = 5068.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180494 restraints weight = 3412.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.182534 restraints weight = 2535.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.184016 restraints weight = 2001.636| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5015 Z= 0.145 Angle : 0.613 7.800 6841 Z= 0.311 Chirality : 0.044 0.170 755 Planarity : 0.004 0.039 875 Dihedral : 5.389 57.797 688 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.01 % Allowed : 21.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.33), residues: 622 helix: -2.04 (0.95), residues: 30 sheet: 1.04 (0.34), residues: 224 loop : -1.13 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 454 TYR 0.011 0.002 TYR b 55 PHE 0.016 0.001 PHE b 77 TRP 0.010 0.001 TRP a 158 HIS 0.002 0.000 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5007) covalent geometry : angle 0.61231 ( 6825) SS BOND : bond 0.00367 ( 8) SS BOND : angle 0.76619 ( 16) hydrogen bonds : bond 0.02981 ( 143) hydrogen bonds : angle 5.42205 ( 393) *********************** 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 142 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8260 (p90) cc_final: 0.7935 (p90) REVERT: A 441 LEU cc_start: 0.7639 (tt) cc_final: 0.7344 (tp) REVERT: A 458 LYS cc_start: 0.8060 (ptmt) cc_final: 0.7045 (mmmt) REVERT: A 468 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 474 GLN cc_start: 0.7245 (mt0) cc_final: 0.6977 (mt0) REVERT: a 19 LYS cc_start: 0.7421 (mttt) cc_final: 0.7084 (pttm) REVERT: a 90 ASP cc_start: 0.7722 (m-30) cc_final: 0.7331 (m-30) REVERT: a 139 MET cc_start: 0.5524 (mmm) cc_final: 0.4979 (mtp) REVERT: b 4 MET cc_start: 0.6431 (mtt) cc_final: 0.6138 (mtt) REVERT: b 210 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7828 (tp) outliers start: 22 outliers final: 18 residues processed: 131 average time/residue: 0.0730 time to fit residues: 12.2509 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 : 0.208 ------------------------------------------------------------------------------- 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 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 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 60 ARG 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 Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 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 439 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 = 0.4313 r_free = 0.4313 target = 0.194615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.172993 restraints weight = 8803.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177239 restraints weight = 5098.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.180176 restraints weight = 3447.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.182244 restraints weight = 2546.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.183655 restraints weight = 2006.720| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5015 Z= 0.148 Angle : 0.636 10.573 6841 Z= 0.318 Chirality : 0.044 0.175 755 Planarity : 0.004 0.035 875 Dihedral : 5.225 47.059 688 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.37 % Allowed : 21.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.33), residues: 622 helix: -1.61 (1.14), residues: 24 sheet: 1.04 (0.34), residues: 225 loop : -1.17 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.015 0.002 TYR A 453 PHE 0.017 0.001 PHE b 77 TRP 0.011 0.001 TRP a 158 HIS 0.002 0.001 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5007) covalent geometry : angle 0.63517 ( 6825) SS BOND : bond 0.00357 ( 8) SS BOND : angle 0.80026 ( 16) hydrogen bonds : bond 0.02998 ( 143) hydrogen bonds : angle 5.38479 ( 393) *********************** 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 141 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8228 (p90) cc_final: 0.7867 (p90) REVERT: A 458 LYS cc_start: 0.8031 (ptmt) cc_final: 0.6972 (mmmt) REVERT: A 468 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7807 (mp) REVERT: A 474 GLN cc_start: 0.7219 (mt0) cc_final: 0.6925 (mt0) REVERT: a 19 LYS cc_start: 0.7472 (mttt) cc_final: 0.7094 (pttm) REVERT: a 41 HIS cc_start: 0.5142 (OUTLIER) cc_final: 0.4888 (m170) REVERT: a 90 ASP cc_start: 0.7767 (m-30) cc_final: 0.7343 (m-30) REVERT: a 139 MET cc_start: 0.5639 (mmm) cc_final: 0.5241 (mtp) REVERT: b 97 TYR cc_start: 0.3611 (OUTLIER) cc_final: 0.2563 (m-80) REVERT: b 210 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7930 (tp) outliers start: 24 outliers final: 19 residues processed: 127 average time/residue: 0.0647 time to fit residues: 10.6685 Evaluate side-chains 135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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 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 181 LEU Chi-restraints excluded: chain a residue 210 VAL 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 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 0.0070 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.195560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174581 restraints weight = 8762.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178656 restraints weight = 5304.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.181385 restraints weight = 3634.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183278 restraints weight = 2731.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.184591 restraints weight = 2189.442| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5015 Z= 0.137 Angle : 0.619 11.853 6841 Z= 0.312 Chirality : 0.044 0.167 755 Planarity : 0.004 0.035 875 Dihedral : 5.015 46.499 688 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.74 % Allowed : 20.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.34), residues: 622 helix: -1.61 (1.15), residues: 24 sheet: 1.09 (0.34), residues: 225 loop : -1.11 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.010 0.001 TYR b 55 PHE 0.017 0.001 PHE b 77 TRP 0.010 0.001 TRP a 158 HIS 0.002 0.001 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5007) covalent geometry : angle 0.61844 ( 6825) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.80642 ( 16) hydrogen bonds : bond 0.02942 ( 143) hydrogen bonds : angle 5.30784 ( 393) *********************** 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 146 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8245 (p90) cc_final: 0.7912 (p90) REVERT: A 458 LYS cc_start: 0.8096 (ptmt) cc_final: 0.7108 (mmmt) REVERT: A 468 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 474 GLN cc_start: 0.7166 (mt0) cc_final: 0.6939 (mt0) REVERT: a 19 LYS cc_start: 0.7415 (mttt) cc_final: 0.7104 (pttm) REVERT: a 41 HIS cc_start: 0.5135 (OUTLIER) cc_final: 0.4884 (m170) REVERT: a 90 ASP cc_start: 0.7749 (m-30) cc_final: 0.7368 (m-30) REVERT: a 139 MET cc_start: 0.5665 (mmm) cc_final: 0.5298 (mtp) REVERT: b 60 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6384 (ptm160) REVERT: b 97 TYR cc_start: 0.3626 (OUTLIER) cc_final: 0.2609 (m-80) REVERT: b 210 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7969 (tp) outliers start: 26 outliers final: 17 residues processed: 132 average time/residue: 0.0697 time to fit residues: 12.0111 Evaluate side-chains 135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 54 ASN 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 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 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 200 ASN ** a 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.194251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.173121 restraints weight = 8889.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.177143 restraints weight = 5339.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.179876 restraints weight = 3684.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.181716 restraints weight = 2778.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.183142 restraints weight = 2235.900| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5015 Z= 0.151 Angle : 0.653 14.170 6841 Z= 0.323 Chirality : 0.044 0.170 755 Planarity : 0.004 0.034 875 Dihedral : 4.978 45.050 686 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.01 % Allowed : 21.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.34), residues: 622 helix: -1.53 (1.18), residues: 24 sheet: 1.17 (0.35), residues: 220 loop : -1.13 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 454 TYR 0.017 0.002 TYR A 495 PHE 0.016 0.001 PHE b 77 TRP 0.010 0.001 TRP b 153 HIS 0.002 0.001 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5007) covalent geometry : angle 0.65258 ( 6825) SS BOND : bond 0.00382 ( 8) SS BOND : angle 0.86184 ( 16) hydrogen bonds : bond 0.03097 ( 143) hydrogen bonds : angle 5.30281 ( 393) ********************** 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 137 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8268 (p90) cc_final: 0.7958 (p90) REVERT: A 379 CYS cc_start: 0.5453 (m) cc_final: 0.5184 (m) REVERT: A 458 LYS cc_start: 0.8149 (ptmt) cc_final: 0.7172 (mmmt) REVERT: A 468 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 474 GLN cc_start: 0.7276 (mt0) cc_final: 0.7011 (mt0) REVERT: a 19 LYS cc_start: 0.7481 (mttt) cc_final: 0.7138 (pttm) REVERT: a 41 HIS cc_start: 0.5159 (OUTLIER) cc_final: 0.4925 (m170) REVERT: a 90 ASP cc_start: 0.7760 (m-30) cc_final: 0.7388 (m-30) REVERT: a 139 MET cc_start: 0.5454 (mmm) cc_final: 0.5228 (mtp) REVERT: a 195 GLU cc_start: 0.6688 (tm-30) cc_final: 0.6273 (tm-30) REVERT: b 97 TYR cc_start: 0.3680 (OUTLIER) cc_final: 0.2638 (m-80) REVERT: b 210 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7983 (tp) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.0720 time to fit residues: 11.9682 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 : 0.248 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 41 HIS 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 197 TYR Chi-restraints excluded: chain b residue 210 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.197052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175516 restraints weight = 8826.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.179866 restraints weight = 5116.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182720 restraints weight = 3441.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.184732 restraints weight = 2558.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.186136 restraints weight = 2028.416| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5015 Z= 0.121 Angle : 0.615 11.015 6841 Z= 0.306 Chirality : 0.044 0.164 755 Planarity : 0.004 0.035 875 Dihedral : 4.803 44.775 686 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.91 % Allowed : 23.13 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.34), residues: 622 helix: -1.57 (1.17), residues: 24 sheet: 1.11 (0.34), residues: 225 loop : -1.06 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 98 TYR 0.029 0.001 TYR A 453 PHE 0.016 0.001 PHE b 77 TRP 0.009 0.001 TRP a 192 HIS 0.003 0.001 HIS a 203 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5007) covalent geometry : angle 0.61427 ( 6825) SS BOND : bond 0.00360 ( 8) SS BOND : angle 0.83999 ( 16) hydrogen bonds : bond 0.02745 ( 143) hydrogen bonds : angle 5.09708 ( 393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1083.18 seconds wall clock time: 19 minutes 29.10 seconds (1169.10 seconds total)