Starting phenix.real_space_refine on Tue Jan 14 00:05:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc1_39919/01_2025/8zc1_39919.cif" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 18 5.16 5 C 2907 2.51 5 N 767 2.21 5 O 878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4570 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1318 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain breaks: 2 Chain: "C" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1661 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.30, per 1000 atoms: 0.72 Number of scatterers: 4570 At special positions: 0 Unit cell: (84.48, 76.56, 120.12, 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 18 16.00 O 878 8.00 N 767 7.00 C 2907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " 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: 0.93 Conformation dependent library (CDL) restraints added in 555.8 milliseconds 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 6.9% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.145A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.518A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.669A pdb=" N GLN C 137 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.635A pdb=" N TRP C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 197 " --> pdb=" O PRO C 193 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 192 through 199' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.894A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 112 removed outlier: 4.025A pdb=" N TRP E 111 " --> pdb=" O CYS E 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.810A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.864A pdb=" N ASP C 86 " --> pdb=" O GLN C 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 12 Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.684A pdb=" N THR C 127 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 146 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 129 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 144 " --> pdb=" O PHE C 129 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 185 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP C 149 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR C 183 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 188 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU C 171 " --> pdb=" O TYR C 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.804A pdb=" N ALA C 184 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.451A pdb=" N TRP C 159 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 156 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 166 removed outlier: 4.451A pdb=" N TRP C 159 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 156 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 202 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 215 " --> pdb=" O CYS C 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.615A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 5 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 20 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP E 73 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.109A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 50 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N CYS E 96 " --> pdb=" O TRP E 117 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP E 117 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 98 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.109A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 50 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.631A pdb=" N SER E 134 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 195 " --> pdb=" O HIS E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 137 removed outlier: 3.631A pdb=" N SER E 134 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 166 through 168 removed outlier: 4.071A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 330 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: 1.34 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1449 1.35 - 1.47: 1259 1.47 - 1.59: 1964 1.59 - 1.71: 0 1.71 - 1.84: 22 Bond restraints: 4694 Sorted by residual: bond pdb=" C LYS E 215 " pdb=" N PRO E 216 " ideal model delta sigma weight residual 1.335 1.382 -0.046 1.30e-02 5.92e+03 1.28e+01 bond pdb=" C VAL B 382 " pdb=" N SER B 383 " ideal model delta sigma weight residual 1.327 1.288 0.039 1.71e-02 3.42e+03 5.13e+00 bond pdb=" N ASP E 158 " pdb=" CA ASP E 158 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.46e+00 bond pdb=" CA THR E 77 " pdb=" CB THR E 77 " ideal model delta sigma weight residual 1.527 1.554 -0.027 1.70e-02 3.46e+03 2.45e+00 bond pdb=" C PHE E 136 " pdb=" N PRO E 137 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.25e-02 6.40e+03 1.60e+00 ... (remaining 4689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6141 1.72 - 3.44: 218 3.44 - 5.17: 24 5.17 - 6.89: 11 6.89 - 8.61: 4 Bond angle restraints: 6398 Sorted by residual: angle pdb=" C ILE E 76 " pdb=" N THR E 77 " pdb=" CA THR E 77 " ideal model delta sigma weight residual 122.46 128.09 -5.63 1.41e+00 5.03e-01 1.60e+01 angle pdb=" C LYS C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C VAL E 125 " pdb=" N SER E 126 " pdb=" CA SER E 126 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA THR E 77 " pdb=" CB THR E 77 " pdb=" CG2 THR E 77 " ideal model delta sigma weight residual 110.50 115.72 -5.22 1.70e+00 3.46e-01 9.42e+00 angle pdb=" CG1 ILE E 76 " pdb=" CB ILE E 76 " pdb=" CG2 ILE E 76 " ideal model delta sigma weight residual 110.70 102.26 8.44 3.00e+00 1.11e-01 7.92e+00 ... (remaining 6393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 2502 16.06 - 32.12: 205 32.12 - 48.19: 47 48.19 - 64.25: 10 64.25 - 80.31: 9 Dihedral angle restraints: 2773 sinusoidal: 1047 harmonic: 1726 Sorted by residual: dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 210 " pdb=" CB CYS E 210 " ideal model delta sinusoidal sigma weight residual 93.00 166.07 -73.07 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 53.44 39.56 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 130.42 -37.42 1 1.00e+01 1.00e-02 1.98e+01 ... (remaining 2770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 514 0.053 - 0.105: 149 0.105 - 0.158: 35 0.158 - 0.210: 1 0.210 - 0.263: 2 Chirality restraints: 701 Sorted by residual: chirality pdb=" CB VAL E 125 " pdb=" CA VAL E 125 " pdb=" CG1 VAL E 125 " pdb=" CG2 VAL E 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE E 76 " pdb=" CA ILE E 76 " pdb=" CG1 ILE E 76 " pdb=" CG2 ILE E 76 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA THR E 77 " pdb=" N THR E 77 " pdb=" C THR E 77 " pdb=" CB THR E 77 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 698 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO B 373 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.018 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR B 495 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.80e+00 pdb=" N PRO B 479 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.027 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1461 2.83 - 3.35: 3742 3.35 - 3.87: 7351 3.87 - 4.38: 7584 4.38 - 4.90: 13612 Nonbonded interactions: 33750 Sorted by model distance: nonbonded pdb=" OG SER B 438 " pdb=" O PRO B 507 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR C 35 " pdb=" O ARG E 110 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP E 57 " pdb=" OG SER E 104 " model vdw 2.323 3.040 nonbonded pdb=" OG SER C 203 " pdb=" OE1 GLU C 214 " model vdw 2.343 3.040 ... (remaining 33745 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 14.930 Find NCS groups from input model: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 0.046 4694 Z= 0.228 Angle : 0.755 8.612 6398 Z= 0.400 Chirality : 0.052 0.263 701 Planarity : 0.005 0.063 821 Dihedral : 13.383 80.311 1648 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.32), residues: 583 helix: -4.58 (0.35), residues: 18 sheet: -0.01 (0.39), residues: 163 loop : -1.50 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 353 HIS 0.005 0.002 HIS C 199 PHE 0.010 0.001 PHE B 400 TYR 0.036 0.001 TYR B 495 ARG 0.003 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.591 Fit side-chains REVERT: B 494 SER cc_start: 0.8642 (p) cc_final: 0.8441 (p) REVERT: E 31 ASP cc_start: 0.7724 (p0) cc_final: 0.7388 (p0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1552 time to fit residues: 14.9159 Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 6 GLN C 39 GLN E 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099207 restraints weight = 16021.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100880 restraints weight = 10913.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101928 restraints weight = 8066.562| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4694 Z= 0.223 Angle : 0.583 6.862 6398 Z= 0.306 Chirality : 0.045 0.141 701 Planarity : 0.005 0.055 821 Dihedral : 4.321 15.104 643 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.33), residues: 583 helix: -4.36 (0.49), residues: 18 sheet: -0.03 (0.35), residues: 186 loop : -1.40 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 36 HIS 0.003 0.001 HIS E 178 PHE 0.011 0.001 PHE B 374 TYR 0.018 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8691 (p) cc_final: 0.8448 (p) REVERT: E 112 MET cc_start: 0.8401 (mmt) cc_final: 0.8199 (mmt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1459 time to fit residues: 11.7929 Evaluate side-chains 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.0060 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.111484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.092072 restraints weight = 16629.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093822 restraints weight = 10900.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095104 restraints weight = 7925.565| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 4694 Z= 0.421 Angle : 0.743 13.265 6398 Z= 0.388 Chirality : 0.049 0.181 701 Planarity : 0.005 0.061 821 Dihedral : 5.395 17.285 643 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.20 % Allowed : 6.37 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 583 helix: -4.08 (0.62), residues: 20 sheet: -0.55 (0.35), residues: 187 loop : -1.49 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 436 HIS 0.008 0.003 HIS C 199 PHE 0.018 0.003 PHE C 64 TYR 0.033 0.002 TYR B 495 ARG 0.005 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 112 MET cc_start: 0.8200 (mmt) cc_final: 0.7870 (mmm) REVERT: E 136 PHE cc_start: 0.7949 (m-80) cc_final: 0.7707 (m-80) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1469 time to fit residues: 11.8403 Evaluate side-chains 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 6 GLN C 195 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.115870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096082 restraints weight = 16468.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.097873 restraints weight = 10761.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099252 restraints weight = 7822.729| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.180 Angle : 0.591 12.324 6398 Z= 0.298 Chirality : 0.046 0.155 701 Planarity : 0.005 0.056 821 Dihedral : 4.502 17.101 643 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.33), residues: 583 helix: -4.19 (0.50), residues: 20 sheet: -0.51 (0.34), residues: 186 loop : -1.30 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 436 HIS 0.002 0.001 HIS C 199 PHE 0.011 0.001 PHE E 136 TYR 0.019 0.001 TYR B 495 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: B 455 LEU cc_start: 0.9362 (tp) cc_final: 0.9159 (tp) REVERT: B 494 SER cc_start: 0.8742 (p) cc_final: 0.8531 (p) REVERT: C 53 ASP cc_start: 0.6923 (p0) cc_final: 0.6599 (p0) REVERT: E 112 MET cc_start: 0.8367 (mmt) cc_final: 0.7988 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1454 time to fit residues: 12.4022 Evaluate side-chains 46 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.116822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096731 restraints weight = 16555.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098558 restraints weight = 10795.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099948 restraints weight = 7808.539| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.167 Angle : 0.578 11.175 6398 Z= 0.287 Chirality : 0.046 0.166 701 Planarity : 0.004 0.056 821 Dihedral : 4.226 14.969 643 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.33), residues: 583 helix: -4.05 (0.55), residues: 20 sheet: -0.37 (0.35), residues: 186 loop : -1.23 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.002 0.001 HIS E 214 PHE 0.006 0.001 PHE B 400 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8674 (p) cc_final: 0.8470 (p) REVERT: E 70 MET cc_start: 0.8184 (ttm) cc_final: 0.7566 (ttm) REVERT: E 112 MET cc_start: 0.8488 (mmt) cc_final: 0.8090 (mmm) REVERT: E 154 CYS cc_start: 0.4450 (p) cc_final: 0.4093 (p) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1544 time to fit residues: 13.6233 Evaluate side-chains 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.115623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096587 restraints weight = 16393.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098186 restraints weight = 11128.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099361 restraints weight = 8250.391| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.197 Angle : 0.587 12.527 6398 Z= 0.292 Chirality : 0.046 0.169 701 Planarity : 0.005 0.054 821 Dihedral : 4.239 15.768 643 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.33), residues: 583 helix: -4.03 (0.55), residues: 20 sheet: -0.30 (0.35), residues: 185 loop : -1.22 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 436 HIS 0.004 0.001 HIS C 199 PHE 0.008 0.001 PHE B 400 TYR 0.015 0.001 TYR B 495 ARG 0.003 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: E 70 MET cc_start: 0.7996 (ttm) cc_final: 0.7442 (ttm) REVERT: E 112 MET cc_start: 0.8542 (mmt) cc_final: 0.8126 (mmm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1449 time to fit residues: 12.1158 Evaluate side-chains 43 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.116052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096260 restraints weight = 16184.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.098116 restraints weight = 10753.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099467 restraints weight = 7820.027| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4694 Z= 0.198 Angle : 0.600 11.903 6398 Z= 0.299 Chirality : 0.046 0.154 701 Planarity : 0.005 0.055 821 Dihedral : 4.219 14.301 643 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.34), residues: 583 helix: -4.01 (0.58), residues: 20 sheet: -0.26 (0.37), residues: 176 loop : -1.18 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 36 HIS 0.004 0.001 HIS C 199 PHE 0.009 0.001 PHE B 497 TYR 0.033 0.001 TYR B 495 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.504 Fit side-chains REVERT: B 494 SER cc_start: 0.8706 (p) cc_final: 0.8482 (p) REVERT: E 112 MET cc_start: 0.8453 (mmt) cc_final: 0.8027 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1671 time to fit residues: 15.1362 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.115322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.095635 restraints weight = 16550.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097354 restraints weight = 10941.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098632 restraints weight = 8026.502| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4694 Z= 0.228 Angle : 0.628 12.726 6398 Z= 0.313 Chirality : 0.046 0.145 701 Planarity : 0.005 0.070 821 Dihedral : 4.432 15.655 643 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.34), residues: 583 helix: -4.01 (0.58), residues: 20 sheet: -0.36 (0.36), residues: 175 loop : -1.20 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 36 HIS 0.005 0.001 HIS C 199 PHE 0.009 0.001 PHE E 136 TYR 0.028 0.001 TYR B 495 ARG 0.003 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8473 (mp0) cc_final: 0.8242 (mp0) REVERT: B 494 SER cc_start: 0.8763 (p) cc_final: 0.8554 (p) REVERT: E 78 THR cc_start: 0.7808 (p) cc_final: 0.7581 (p) REVERT: E 112 MET cc_start: 0.8505 (mmt) cc_final: 0.8054 (mmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1449 time to fit residues: 13.1148 Evaluate side-chains 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.092376 restraints weight = 16311.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094072 restraints weight = 10982.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095280 restraints weight = 8089.967| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4694 Z= 0.315 Angle : 0.677 13.709 6398 Z= 0.342 Chirality : 0.047 0.165 701 Planarity : 0.006 0.064 821 Dihedral : 4.853 15.344 643 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.34), residues: 583 helix: -4.04 (0.62), residues: 20 sheet: -0.58 (0.36), residues: 181 loop : -1.26 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 436 HIS 0.006 0.002 HIS C 199 PHE 0.010 0.002 PHE C 64 TYR 0.029 0.002 TYR B 495 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 PHE cc_start: 0.7569 (m-80) cc_final: 0.7265 (m-80) REVERT: E 112 MET cc_start: 0.8452 (mmt) cc_final: 0.8072 (mmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1594 time to fit residues: 12.8771 Evaluate side-chains 44 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.113794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093714 restraints weight = 15963.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.095470 restraints weight = 10706.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096754 restraints weight = 7855.596| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4694 Z= 0.227 Angle : 0.642 14.006 6398 Z= 0.319 Chirality : 0.046 0.139 701 Planarity : 0.005 0.062 821 Dihedral : 4.583 15.737 643 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.34), residues: 583 helix: -4.04 (0.59), residues: 20 sheet: -0.38 (0.37), residues: 181 loop : -1.34 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 36 HIS 0.004 0.002 HIS C 199 PHE 0.009 0.001 PHE E 136 TYR 0.024 0.001 TYR B 495 ARG 0.003 0.001 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1166 Ramachandran restraints generated. 583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 PHE cc_start: 0.7600 (m-80) cc_final: 0.7325 (m-80) REVERT: E 43 GLN cc_start: 0.7891 (pm20) cc_final: 0.7685 (pm20) REVERT: E 78 THR cc_start: 0.7799 (p) cc_final: 0.7572 (p) REVERT: E 112 MET cc_start: 0.8424 (mmt) cc_final: 0.7726 (mmm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1575 time to fit residues: 12.7176 Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 45 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 6 GLN E 178 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094619 restraints weight = 15942.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.096390 restraints weight = 10591.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097667 restraints weight = 7717.113| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4694 Z= 0.188 Angle : 0.639 12.381 6398 Z= 0.314 Chirality : 0.046 0.178 701 Planarity : 0.005 0.062 821 Dihedral : 4.416 14.789 643 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.34), residues: 583 helix: -3.96 (0.62), residues: 20 sheet: -0.49 (0.36), residues: 185 loop : -1.31 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 436 HIS 0.003 0.001 HIS C 199 PHE 0.012 0.001 PHE B 374 TYR 0.025 0.001 TYR B 495 ARG 0.003 0.001 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.43 seconds wall clock time: 31 minutes 53.94 seconds (1913.94 seconds total)