Starting phenix.real_space_refine on Sat Aug 23 05:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g12_29659/08_2025/8g12_29659.map" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 48 5.16 5 C 6296 2.51 5 N 1736 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2495 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'CSO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9980 At special positions: 0 Unit cell: (92.685, 98.53, 91.015, 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 48 16.00 O 1900 8.00 N 1736 7.00 C 6296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.83 Conformation dependent library (CDL) restraints added in 268.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 36.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.628A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.635A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.641A pdb=" N TYR A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.818A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.509A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.628A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.635A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.641A pdb=" N TYR B 140 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.818A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.508A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.628A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.635A pdb=" N ALA C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.641A pdb=" N TYR C 140 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.817A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.508A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.628A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.634A pdb=" N ALA D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.641A pdb=" N TYR D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.818A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.509A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.275A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.738A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 177 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.497A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.402A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 10.274A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.736A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR B 177 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 12.496A pdb=" N PHE B 307 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 11.402A pdb=" N GLY B 300 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N LYS B 309 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY B 298 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63 removed outlier: 10.274A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.737A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 177 " --> pdb=" O MET C 231 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.496A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 10.274A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.737A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 177 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.497A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.402A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1224 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: 1.71 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2821 1.33 - 1.45: 1630 1.45 - 1.57: 5641 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 10180 Sorted by residual: bond pdb=" SG CSO B 152 " pdb=" OD CSO B 152 " ideal model delta sigma weight residual 1.668 1.735 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" SG CSO C 152 " pdb=" OD CSO C 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" SG CSO A 152 " pdb=" OD CSO A 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" SG CSO D 152 " pdb=" OD CSO D 152 " ideal model delta sigma weight residual 1.668 1.734 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N ILE A 206 " pdb=" CA ILE A 206 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.28e-02 6.10e+03 8.95e+00 ... (remaining 10175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 12710 1.49 - 2.97: 883 2.97 - 4.46: 159 4.46 - 5.95: 44 5.95 - 7.44: 12 Bond angle restraints: 13808 Sorted by residual: angle pdb=" N ILE A 206 " pdb=" CA ILE A 206 " pdb=" C ILE A 206 " ideal model delta sigma weight residual 111.56 107.15 4.41 8.60e-01 1.35e+00 2.63e+01 angle pdb=" N ILE B 206 " pdb=" CA ILE B 206 " pdb=" C ILE B 206 " ideal model delta sigma weight residual 111.56 107.16 4.40 8.60e-01 1.35e+00 2.62e+01 angle pdb=" N ILE C 206 " pdb=" CA ILE C 206 " pdb=" C ILE C 206 " ideal model delta sigma weight residual 111.56 107.17 4.39 8.60e-01 1.35e+00 2.61e+01 angle pdb=" N ILE D 206 " pdb=" CA ILE D 206 " pdb=" C ILE D 206 " ideal model delta sigma weight residual 111.56 107.17 4.39 8.60e-01 1.35e+00 2.60e+01 angle pdb=" C ALA D 150 " pdb=" CA ALA D 150 " pdb=" CB ALA D 150 " ideal model delta sigma weight residual 116.34 110.47 5.87 1.40e+00 5.10e-01 1.76e+01 ... (remaining 13803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5440 17.75 - 35.49: 411 35.49 - 53.24: 101 53.24 - 70.99: 36 70.99 - 88.73: 16 Dihedral angle restraints: 6004 sinusoidal: 2228 harmonic: 3776 Sorted by residual: dihedral pdb=" CA VAL A 178 " pdb=" C VAL A 178 " pdb=" N HIS A 179 " pdb=" CA HIS A 179 " ideal model delta harmonic sigma weight residual -180.00 -164.53 -15.47 0 5.00e+00 4.00e-02 9.58e+00 dihedral pdb=" CA VAL B 178 " pdb=" C VAL B 178 " pdb=" N HIS B 179 " pdb=" CA HIS B 179 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CA VAL D 178 " pdb=" C VAL D 178 " pdb=" N HIS D 179 " pdb=" CA HIS D 179 " ideal model delta harmonic sigma weight residual -180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 ... (remaining 6001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 982 0.040 - 0.080: 343 0.080 - 0.119: 189 0.119 - 0.159: 50 0.159 - 0.199: 8 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ILE B 206 " pdb=" N ILE B 206 " pdb=" C ILE B 206 " pdb=" CB ILE B 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA ILE A 206 " pdb=" N ILE A 206 " pdb=" C ILE A 206 " pdb=" CB ILE A 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA ILE C 206 " pdb=" N ILE C 206 " pdb=" C ILE C 206 " pdb=" CB ILE C 206 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1569 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 244 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" CG ASP A 244 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP A 244 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 244 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 244 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" CG ASP D 244 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP D 244 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP D 244 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 244 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" CG ASP B 244 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP B 244 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 244 " -0.016 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 3808 2.90 - 3.40: 9252 3.40 - 3.90: 16520 3.90 - 4.40: 19184 4.40 - 4.90: 32520 Nonbonded interactions: 81284 Sorted by model distance: nonbonded pdb=" O GLY C 201 " pdb=" ND2 ASN C 205 " model vdw 2.394 3.120 nonbonded pdb=" O GLY A 201 " pdb=" ND2 ASN A 205 " model vdw 2.394 3.120 nonbonded pdb=" O GLY D 201 " pdb=" ND2 ASN D 205 " model vdw 2.395 3.120 nonbonded pdb=" O GLY B 201 " pdb=" ND2 ASN B 205 " model vdw 2.395 3.120 nonbonded pdb=" OE2 GLU C 172 " pdb=" NH2 ARG C 248 " model vdw 2.435 3.120 ... (remaining 81279 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.320 Find NCS groups from input model: 0.080 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:9.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 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 : 0.006 0.067 10180 Z= 0.375 Angle : 0.872 7.436 13808 Z= 0.569 Chirality : 0.055 0.199 1572 Planarity : 0.006 0.068 1796 Dihedral : 14.955 88.733 3596 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.38 % Allowed : 13.08 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.23), residues: 1316 helix: -1.32 (0.22), residues: 352 sheet: 0.24 (0.38), residues: 220 loop : -0.88 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 234 TYR 0.005 0.001 TYR A 276 PHE 0.010 0.001 PHE D 286 TRP 0.005 0.001 TRP C 87 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00567 (10180) covalent geometry : angle 0.87165 (13808) hydrogen bonds : bond 0.18720 ( 440) hydrogen bonds : angle 8.02717 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.393 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 0.7143 time to fit residues: 53.6467 Evaluate side-chains 50 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.0020 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.039747 restraints weight = 30939.530| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.94 r_work: 0.2573 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10180 Z= 0.119 Angle : 0.497 6.570 13808 Z= 0.272 Chirality : 0.044 0.127 1572 Planarity : 0.005 0.049 1796 Dihedral : 3.935 14.653 1412 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.48 % Allowed : 12.12 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.24), residues: 1316 helix: 0.91 (0.27), residues: 352 sheet: 0.41 (0.38), residues: 220 loop : -0.45 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 80 TYR 0.012 0.001 TYR A 314 PHE 0.006 0.001 PHE D 11 TRP 0.004 0.001 TRP C 313 HIS 0.003 0.000 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00258 (10180) covalent geometry : angle 0.49659 (13808) hydrogen bonds : bond 0.03567 ( 440) hydrogen bonds : angle 5.72101 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.288 Fit side-chains REVERT: A 264 GLN cc_start: 0.9176 (tt0) cc_final: 0.8861 (tm-30) REVERT: B 264 GLN cc_start: 0.9168 (tt0) cc_final: 0.8828 (tm-30) REVERT: C 264 GLN cc_start: 0.9219 (tt0) cc_final: 0.8930 (tm-30) REVERT: D 264 GLN cc_start: 0.9146 (tt0) cc_final: 0.8830 (tm-30) outliers start: 5 outliers final: 0 residues processed: 61 average time/residue: 0.5482 time to fit residues: 35.7844 Evaluate side-chains 53 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.043385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.034517 restraints weight = 32200.283| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 2.82 r_work: 0.2409 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9368 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 10180 Z= 0.297 Angle : 0.624 9.257 13808 Z= 0.343 Chirality : 0.048 0.168 1572 Planarity : 0.005 0.054 1796 Dihedral : 4.389 19.104 1412 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.73 % Allowed : 12.21 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.24), residues: 1316 helix: 1.36 (0.28), residues: 356 sheet: 0.18 (0.37), residues: 232 loop : -0.30 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 80 TYR 0.015 0.001 TYR D 314 PHE 0.015 0.002 PHE C 318 TRP 0.008 0.001 TRP A 313 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00692 (10180) covalent geometry : angle 0.62442 (13808) hydrogen bonds : bond 0.04767 ( 440) hydrogen bonds : angle 5.85544 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.306 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 71 average time/residue: 0.5664 time to fit residues: 43.0123 Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 237 THR Chi-restraints excluded: chain D residue 244 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.046524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.037679 restraints weight = 31417.432| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.88 r_work: 0.2510 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2393 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9299 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10180 Z= 0.091 Angle : 0.487 5.880 13808 Z= 0.262 Chirality : 0.043 0.128 1572 Planarity : 0.004 0.056 1796 Dihedral : 3.983 16.892 1412 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.25 % Allowed : 12.50 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1316 helix: 1.79 (0.28), residues: 352 sheet: 0.52 (0.37), residues: 224 loop : -0.31 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 80 TYR 0.008 0.001 TYR A 314 PHE 0.005 0.001 PHE D 286 TRP 0.005 0.001 TRP A 313 HIS 0.002 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00195 (10180) covalent geometry : angle 0.48712 (13808) hydrogen bonds : bond 0.02994 ( 440) hydrogen bonds : angle 5.42071 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.379 Fit side-chains outliers start: 13 outliers final: 1 residues processed: 65 average time/residue: 0.6119 time to fit residues: 42.5289 Evaluate side-chains 54 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.034869 restraints weight = 32073.701| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.84 r_work: 0.2418 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2300 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9359 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 10180 Z= 0.243 Angle : 0.578 8.942 13808 Z= 0.316 Chirality : 0.047 0.163 1572 Planarity : 0.005 0.059 1796 Dihedral : 4.219 19.322 1412 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.06 % Allowed : 13.65 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1316 helix: 1.70 (0.28), residues: 356 sheet: 0.40 (0.37), residues: 224 loop : -0.25 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 80 TYR 0.013 0.001 TYR C 314 PHE 0.010 0.001 PHE D 286 TRP 0.007 0.001 TRP A 313 HIS 0.004 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00567 (10180) covalent geometry : angle 0.57842 (13808) hydrogen bonds : bond 0.04194 ( 440) hydrogen bonds : angle 5.63951 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.397 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.6155 time to fit residues: 40.7193 Evaluate side-chains 60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.045302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.036429 restraints weight = 31834.516| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 2.86 r_work: 0.2469 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2351 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10180 Z= 0.125 Angle : 0.507 7.267 13808 Z= 0.275 Chirality : 0.044 0.129 1572 Planarity : 0.005 0.064 1796 Dihedral : 4.054 19.021 1412 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.48 % Allowed : 14.90 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1316 helix: 1.89 (0.28), residues: 352 sheet: 0.44 (0.37), residues: 224 loop : -0.25 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 80 TYR 0.009 0.001 TYR A 314 PHE 0.007 0.001 PHE D 286 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00285 (10180) covalent geometry : angle 0.50737 (13808) hydrogen bonds : bond 0.03336 ( 440) hydrogen bonds : angle 5.42060 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.352 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.6681 time to fit residues: 40.6760 Evaluate side-chains 57 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS C 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.037175 restraints weight = 31575.885| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 2.89 r_work: 0.2493 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10180 Z= 0.105 Angle : 0.494 6.774 13808 Z= 0.267 Chirality : 0.044 0.128 1572 Planarity : 0.005 0.069 1796 Dihedral : 3.902 18.816 1412 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.58 % Allowed : 14.90 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1316 helix: 2.00 (0.28), residues: 352 sheet: 0.48 (0.37), residues: 224 loop : -0.21 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 80 TYR 0.008 0.001 TYR C 314 PHE 0.005 0.001 PHE D 286 TRP 0.007 0.001 TRP A 313 HIS 0.003 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00238 (10180) covalent geometry : angle 0.49365 (13808) hydrogen bonds : bond 0.02983 ( 440) hydrogen bonds : angle 5.20998 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.288 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.6375 time to fit residues: 42.1584 Evaluate side-chains 60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 13 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.036654 restraints weight = 31540.669| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.85 r_work: 0.2476 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9319 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10180 Z= 0.128 Angle : 0.511 7.153 13808 Z= 0.277 Chirality : 0.044 0.128 1572 Planarity : 0.005 0.075 1796 Dihedral : 3.954 19.136 1412 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.48 % Allowed : 14.90 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1316 helix: 1.98 (0.28), residues: 352 sheet: 0.49 (0.36), residues: 224 loop : -0.27 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 80 TYR 0.009 0.001 TYR C 314 PHE 0.006 0.001 PHE D 286 TRP 0.007 0.001 TRP C 313 HIS 0.004 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00293 (10180) covalent geometry : angle 0.51087 (13808) hydrogen bonds : bond 0.03226 ( 440) hydrogen bonds : angle 5.25105 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.291 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.6745 time to fit residues: 41.7847 Evaluate side-chains 57 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.036107 restraints weight = 31689.004| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 2.89 r_work: 0.2459 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9332 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10180 Z= 0.144 Angle : 0.526 7.904 13808 Z= 0.285 Chirality : 0.045 0.130 1572 Planarity : 0.005 0.078 1796 Dihedral : 4.037 20.580 1412 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.77 % Allowed : 14.71 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1316 helix: 1.97 (0.28), residues: 352 sheet: 0.51 (0.37), residues: 224 loop : -0.28 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 80 TYR 0.010 0.001 TYR C 314 PHE 0.007 0.001 PHE D 286 TRP 0.006 0.001 TRP A 313 HIS 0.004 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00331 (10180) covalent geometry : angle 0.52641 (13808) hydrogen bonds : bond 0.03406 ( 440) hydrogen bonds : angle 5.30339 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.409 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.6598 time to fit residues: 42.9118 Evaluate side-chains 58 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 0.0770 chunk 100 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.045799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.036870 restraints weight = 31370.231| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.83 r_work: 0.2483 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2365 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9317 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10180 Z= 0.118 Angle : 0.508 7.137 13808 Z= 0.274 Chirality : 0.044 0.128 1572 Planarity : 0.005 0.081 1796 Dihedral : 3.979 20.652 1412 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.48 % Allowed : 15.00 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.25), residues: 1316 helix: 2.05 (0.27), residues: 352 sheet: 0.53 (0.37), residues: 224 loop : -0.26 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 80 TYR 0.008 0.001 TYR A 314 PHE 0.006 0.001 PHE C 286 TRP 0.006 0.001 TRP C 313 HIS 0.003 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00270 (10180) covalent geometry : angle 0.50800 (13808) hydrogen bonds : bond 0.03119 ( 440) hydrogen bonds : angle 5.23101 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.370 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 0.6231 time to fit residues: 38.6285 Evaluate side-chains 57 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain D residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.044366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.035279 restraints weight = 31889.938| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 2.90 r_work: 0.2431 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9349 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10180 Z= 0.189 Angle : 0.557 8.726 13808 Z= 0.302 Chirality : 0.046 0.146 1572 Planarity : 0.005 0.081 1796 Dihedral : 4.181 21.816 1412 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.58 % Allowed : 15.00 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1316 helix: 2.02 (0.27), residues: 352 sheet: 0.46 (0.37), residues: 224 loop : -0.29 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 80 TYR 0.011 0.001 TYR C 314 PHE 0.008 0.001 PHE A 286 TRP 0.006 0.001 TRP C 313 HIS 0.005 0.001 HIS B 179 Details of bonding type rmsd covalent geometry : bond 0.00440 (10180) covalent geometry : angle 0.55673 (13808) hydrogen bonds : bond 0.03804 ( 440) hydrogen bonds : angle 5.43955 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3342.80 seconds wall clock time: 57 minutes 47.24 seconds (3467.24 seconds total)