Starting phenix.real_space_refine on Sun Apr 27 05:21:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc1_39919/04_2025/8zc1_39919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc1_39919/04_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_39919/04_2025/8zc1_39919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc1_39919/04_2025/8zc1_39919.map" model { file = "/net/cci-nas-00/data/ceres_data/8zc1_39919/04_2025/8zc1_39919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc1_39919/04_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-5669/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: 3.45, per 1000 atoms: 0.75 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: 0.95 Conformation dependent library (CDL) restraints added in 579.1 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: 0.70 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: 1.16 Time building geometry restraints manager: 1.16 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: 3.170 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: 0.060 Process input model: 14.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- 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 4701 Z= 0.176 Angle : 0.756 8.612 6412 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 Details of bonding type rmsd hydrogen bonds : bond 0.29842 ( 107) hydrogen bonds : angle 10.80937 ( 330) SS BOND : bond 0.00503 ( 7) SS BOND : angle 1.18527 ( 14) covalent geometry : bond 0.00346 ( 4694) covalent geometry : angle 0.75495 ( 6398) *********************** 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 : 0.528 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: 0.1424 time to fit residues: 13.6805 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 : 0.522 ------------------------------------------------------------------------------- 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 = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099254 restraints weight = 16021.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100865 restraints weight = 10874.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.102080 restraints weight = 8051.303| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 4701 Z= 0.154 Angle : 0.584 6.862 6412 Z= 0.307 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 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 107) hydrogen bonds : angle 7.08546 ( 330) SS BOND : bond 0.00429 ( 7) SS BOND : angle 0.99182 ( 14) covalent geometry : bond 0.00338 ( 4694) covalent geometry : angle 0.58275 ( 6398) *********************** 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 : 0.523 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8693 (p) cc_final: 0.8452 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1486 time to fit residues: 12.1747 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 : 0.499 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.116137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096936 restraints weight = 16362.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098545 restraints weight = 11207.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099776 restraints weight = 8348.405| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4701 Z= 0.164 Angle : 0.593 10.299 6412 Z= 0.305 Chirality : 0.046 0.158 701 Planarity : 0.005 0.055 821 Dihedral : 4.397 14.507 643 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 (0.33), residues: 583 helix: -4.38 (0.47), residues: 18 sheet: -0.18 (0.35), residues: 185 loop : -1.33 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.005 0.002 HIS C 199 PHE 0.012 0.002 PHE B 374 TYR 0.027 0.001 TYR B 495 ARG 0.003 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 107) hydrogen bonds : angle 6.17233 ( 330) SS BOND : bond 0.00522 ( 7) SS BOND : angle 1.10931 ( 14) covalent geometry : bond 0.00362 ( 4694) covalent geometry : angle 0.59088 ( 6398) *********************** 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 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1415 time to fit residues: 10.8550 Evaluate side-chains 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 0.0470 chunk 23 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 C 39 GLN ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.118113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.098016 restraints weight = 16429.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099914 restraints weight = 10731.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101301 restraints weight = 7734.867| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4701 Z= 0.111 Angle : 0.554 11.102 6412 Z= 0.278 Chirality : 0.045 0.147 701 Planarity : 0.004 0.053 821 Dihedral : 4.071 15.766 643 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 (0.33), residues: 583 helix: -4.04 (0.54), residues: 20 sheet: -0.22 (0.34), residues: 195 loop : -1.24 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 436 HIS 0.002 0.001 HIS E 214 PHE 0.008 0.001 PHE B 497 TYR 0.019 0.001 TYR B 495 ARG 0.002 0.000 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 107) hydrogen bonds : angle 5.73184 ( 330) SS BOND : bond 0.00456 ( 7) SS BOND : angle 0.89223 ( 14) covalent geometry : bond 0.00250 ( 4694) covalent geometry : angle 0.55290 ( 6398) *********************** 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 62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8722 (p) cc_final: 0.8443 (p) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1392 time to fit residues: 11.8397 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 : 0.524 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.116560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097130 restraints weight = 16501.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098987 restraints weight = 10766.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100358 restraints weight = 7761.999| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4701 Z= 0.122 Angle : 0.557 10.303 6412 Z= 0.280 Chirality : 0.045 0.163 701 Planarity : 0.004 0.053 821 Dihedral : 4.025 14.401 643 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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: -1.34 (0.33), residues: 583 helix: -3.86 (0.61), residues: 20 sheet: -0.18 (0.35), residues: 186 loop : -1.12 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 436 HIS 0.003 0.001 HIS E 214 PHE 0.008 0.001 PHE B 374 TYR 0.016 0.001 TYR B 495 ARG 0.002 0.000 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.02999 ( 107) hydrogen bonds : angle 5.49680 ( 330) SS BOND : bond 0.00407 ( 7) SS BOND : angle 0.86700 ( 14) covalent geometry : bond 0.00272 ( 4694) covalent geometry : angle 0.55645 ( 6398) *********************** 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 62 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 SER cc_start: 0.8711 (p) cc_final: 0.8470 (p) REVERT: E 70 MET cc_start: 0.8273 (ttm) cc_final: 0.7678 (ttm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1279 time to fit residues: 10.9804 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 : 0.513 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.116950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.097439 restraints weight = 16288.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.099361 restraints weight = 10506.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100706 restraints weight = 7498.399| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4701 Z= 0.117 Angle : 0.569 10.816 6412 Z= 0.284 Chirality : 0.045 0.171 701 Planarity : 0.004 0.053 821 Dihedral : 4.012 15.163 643 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -1.29 (0.34), residues: 583 helix: -3.68 (0.71), residues: 20 sheet: -0.16 (0.35), residues: 195 loop : -1.10 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 436 HIS 0.002 0.001 HIS E 214 PHE 0.007 0.001 PHE B 400 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 107) hydrogen bonds : angle 5.46998 ( 330) SS BOND : bond 0.00447 ( 7) SS BOND : angle 1.06657 ( 14) covalent geometry : bond 0.00265 ( 4694) covalent geometry : angle 0.56701 ( 6398) *********************** 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 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 SER cc_start: 0.8709 (p) cc_final: 0.8474 (p) REVERT: E 70 MET cc_start: 0.8290 (ttm) cc_final: 0.8027 (ttm) REVERT: E 154 CYS cc_start: 0.4507 (p) cc_final: 0.4124 (p) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1234 time to fit residues: 11.0892 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 : 0.497 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 1 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.118083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.098652 restraints weight = 16291.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100491 restraints weight = 10738.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.101876 restraints weight = 7782.324| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4701 Z= 0.097 Angle : 0.555 9.374 6412 Z= 0.274 Chirality : 0.045 0.154 701 Planarity : 0.004 0.052 821 Dihedral : 3.866 13.945 643 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -1.20 (0.34), residues: 583 helix: -3.51 (0.80), residues: 20 sheet: -0.08 (0.35), residues: 197 loop : -1.06 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 36 HIS 0.002 0.001 HIS E 35 PHE 0.013 0.001 PHE E 136 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 107) hydrogen bonds : angle 5.27509 ( 330) SS BOND : bond 0.00428 ( 7) SS BOND : angle 0.99226 ( 14) covalent geometry : bond 0.00219 ( 4694) covalent geometry : angle 0.55338 ( 6398) *********************** 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 64 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 494 SER cc_start: 0.8622 (p) cc_final: 0.8414 (p) REVERT: C 202 TYR cc_start: 0.5211 (m-80) cc_final: 0.4686 (m-80) REVERT: E 36 TRP cc_start: 0.8125 (m-10) cc_final: 0.7747 (m-10) REVERT: E 112 MET cc_start: 0.8275 (mmt) cc_final: 0.8069 (mmm) REVERT: E 154 CYS cc_start: 0.4452 (p) cc_final: 0.4043 (p) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1234 time to fit residues: 11.0448 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 : 0.568 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.115788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096233 restraints weight = 16493.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.098093 restraints weight = 10611.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099513 restraints weight = 7643.275| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4701 Z= 0.140 Angle : 0.581 10.635 6412 Z= 0.290 Chirality : 0.045 0.156 701 Planarity : 0.004 0.053 821 Dihedral : 4.066 14.769 643 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -1.21 (0.34), residues: 583 helix: -3.62 (0.74), residues: 20 sheet: -0.08 (0.36), residues: 185 loop : -1.04 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 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 B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 107) hydrogen bonds : angle 5.43569 ( 330) SS BOND : bond 0.00421 ( 7) SS BOND : angle 1.03671 ( 14) covalent geometry : bond 0.00316 ( 4694) covalent geometry : angle 0.57927 ( 6398) *********************** 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 63 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: E 78 THR cc_start: 0.8032 (p) cc_final: 0.7805 (p) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1360 time to fit residues: 11.8057 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 : 0.546 ------------------------------------------------------------------------------- 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: 7.9990 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3865 r_free = 0.3865 target = 0.115290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095834 restraints weight = 16266.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097668 restraints weight = 10622.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098987 restraints weight = 7661.716| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4701 Z= 0.137 Angle : 0.592 11.116 6412 Z= 0.294 Chirality : 0.045 0.151 701 Planarity : 0.004 0.053 821 Dihedral : 4.199 16.363 643 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -1.20 (0.34), residues: 583 helix: -3.69 (0.71), residues: 20 sheet: -0.10 (0.36), residues: 185 loop : -1.01 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 36 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 0.004 0.000 ARG C 62 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 107) hydrogen bonds : angle 5.47470 ( 330) SS BOND : bond 0.00431 ( 7) SS BOND : angle 1.00843 ( 14) covalent geometry : bond 0.00311 ( 4694) covalent geometry : angle 0.59083 ( 6398) *********************** 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 : 0.497 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8670 (p) cc_final: 0.8456 (p) REVERT: E 78 THR cc_start: 0.8015 (p) cc_final: 0.7801 (p) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1271 time to fit residues: 10.9199 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 : 0.463 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.117303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098011 restraints weight = 16233.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099818 restraints weight = 10713.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101132 restraints weight = 7785.832| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4701 Z= 0.104 Angle : 0.579 11.208 6412 Z= 0.286 Chirality : 0.046 0.152 701 Planarity : 0.004 0.052 821 Dihedral : 3.956 16.213 643 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.27 (0.34), residues: 583 helix: -3.70 (0.71), residues: 20 sheet: -0.13 (0.34), residues: 202 loop : -1.11 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 36 HIS 0.002 0.001 HIS C 199 PHE 0.010 0.001 PHE B 497 TYR 0.033 0.001 TYR B 495 ARG 0.003 0.000 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 107) hydrogen bonds : angle 5.28466 ( 330) SS BOND : bond 0.00390 ( 7) SS BOND : angle 0.82741 ( 14) covalent geometry : bond 0.00238 ( 4694) covalent geometry : angle 0.57836 ( 6398) ********************** 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 65 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 494 SER cc_start: 0.8679 (p) cc_final: 0.8415 (p) REVERT: E 46 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7981 (mm-30) REVERT: E 78 THR cc_start: 0.8050 (p) cc_final: 0.7834 (p) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1382 time to fit residues: 12.3223 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 : 0.467 ------------------------------------------------------------------------------- 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: 2.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.114929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095675 restraints weight = 16297.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.097439 restraints weight = 10899.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.098695 restraints weight = 7943.614| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4701 Z= 0.155 Angle : 0.615 11.501 6412 Z= 0.308 Chirality : 0.046 0.154 701 Planarity : 0.005 0.054 821 Dihedral : 4.266 15.894 643 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.54 (0.33), residues: 583 helix: -4.08 (0.56), residues: 26 sheet: -0.16 (0.35), residues: 192 loop : -1.30 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 36 HIS 0.006 0.001 HIS C 199 PHE 0.010 0.002 PHE B 497 TYR 0.030 0.001 TYR B 495 ARG 0.004 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 107) hydrogen bonds : angle 5.41922 ( 330) SS BOND : bond 0.00433 ( 7) SS BOND : angle 1.03900 ( 14) covalent geometry : bond 0.00350 ( 4694) covalent geometry : angle 0.61412 ( 6398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.95 seconds wall clock time: 32 minutes 20.75 seconds (1940.75 seconds total)