Starting phenix.real_space_refine on Wed Apr 30 20:56:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g12_29659/04_2025/8g12_29659_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g12_29659/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g12_29659/04_2025/8g12_29659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g12_29659/04_2025/8g12_29659.map" model { file = "/net/cci-nas-00/data/ceres_data/8g12_29659/04_2025/8g12_29659_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g12_29659/04_2025/8g12_29659_neut.cif" } resolution = 2.17 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'CSO:plan-1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: C, B, D Time building chain proxies: 5.01, per 1000 atoms: 0.50 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.41 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: 3.30 Time building geometry restraints manager: 3.24 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 14.090 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.740 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:15.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.850 ------------------------------------------------------------------------------- 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 (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: -1.26 (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 TRP 0.005 0.001 TRP C 87 HIS 0.002 0.001 HIS A 165 PHE 0.010 0.001 PHE D 286 TYR 0.005 0.001 TYR A 276 ARG 0.003 0.001 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.18720 ( 440) hydrogen bonds : angle 8.02717 ( 1224) covalent geometry : bond 0.00567 (10180) covalent geometry : angle 0.87165 (13808) *********************** 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 : 1.148 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 1.5976 time to fit residues: 120.8183 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 : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 0.0020 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 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 = 0.2953 r_free = 0.2953 target = 0.047848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.038924 restraints weight = 30695.484| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.87 r_work: 0.2552 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9208 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10180 Z= 0.131 Angle : 0.510 6.656 13808 Z= 0.280 Chirality : 0.044 0.134 1572 Planarity : 0.005 0.048 1796 Dihedral : 3.987 15.669 1412 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.58 % Allowed : 12.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1316 helix: 0.95 (0.27), residues: 352 sheet: 0.35 (0.37), residues: 220 loop : -0.44 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 313 HIS 0.004 0.001 HIS D 53 PHE 0.007 0.001 PHE A 11 TYR 0.012 0.001 TYR A 314 ARG 0.009 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 440) hydrogen bonds : angle 5.69573 ( 1224) covalent geometry : bond 0.00293 (10180) covalent geometry : angle 0.51036 (13808) *********************** 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 60 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 1.308 Fit side-chains REVERT: A 264 GLN cc_start: 0.9160 (tt0) cc_final: 0.8829 (tm-30) REVERT: B 264 GLN cc_start: 0.9150 (tt0) cc_final: 0.8820 (tm-30) REVERT: C 264 GLN cc_start: 0.9192 (tt0) cc_final: 0.8846 (tm-30) REVERT: D 264 GLN cc_start: 0.9143 (tt0) cc_final: 0.8851 (tm-30) outliers start: 6 outliers final: 0 residues processed: 59 average time/residue: 1.9340 time to fit residues: 122.2373 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 : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 109 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** 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 = 0.2858 r_free = 0.2858 target = 0.044194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.035137 restraints weight = 31979.251| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 2.88 r_work: 0.2431 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9355 moved from start: 0.1830 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= 0.237 Angle : 0.582 8.496 13808 Z= 0.320 Chirality : 0.047 0.165 1572 Planarity : 0.005 0.054 1796 Dihedral : 4.261 18.935 1412 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.06 % Allowed : 12.31 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.24), residues: 1316 helix: 1.42 (0.28), residues: 356 sheet: 0.41 (0.37), residues: 224 loop : -0.30 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 313 HIS 0.004 0.001 HIS C 53 PHE 0.013 0.001 PHE C 318 TYR 0.013 0.001 TYR A 314 ARG 0.011 0.001 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 440) hydrogen bonds : angle 5.74768 ( 1224) covalent geometry : bond 0.00551 (10180) covalent geometry : angle 0.58195 (13808) *********************** 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 64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.217 Fit side-chains outliers start: 11 outliers final: 12 residues processed: 64 average time/residue: 1.4390 time to fit residues: 99.0885 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 244 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 LEU 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 244 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 195 LEU 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 86 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 HIS ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.045397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.036422 restraints weight = 31225.312| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.86 r_work: 0.2474 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9323 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10180 Z= 0.128 Angle : 0.508 7.017 13808 Z= 0.276 Chirality : 0.044 0.138 1572 Planarity : 0.005 0.055 1796 Dihedral : 4.064 17.670 1412 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.92 % Allowed : 11.15 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.25), residues: 1316 helix: 1.75 (0.28), residues: 352 sheet: 0.46 (0.37), residues: 224 loop : -0.27 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.002 0.000 HIS C 53 PHE 0.007 0.001 PHE D 286 TYR 0.009 0.001 TYR B 314 ARG 0.013 0.001 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 440) hydrogen bonds : angle 5.50096 ( 1224) covalent geometry : bond 0.00292 (10180) covalent geometry : angle 0.50831 (13808) *********************** 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 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 1.178 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 70 average time/residue: 1.4099 time to fit residues: 105.7366 Evaluate side-chains 59 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.044443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.035431 restraints weight = 31632.014| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 2.88 r_work: 0.2441 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2323 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9346 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10180 Z= 0.182 Angle : 0.541 7.983 13808 Z= 0.295 Chirality : 0.045 0.153 1572 Planarity : 0.005 0.058 1796 Dihedral : 4.113 18.968 1412 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.54 % Allowed : 12.12 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.25), residues: 1316 helix: 1.74 (0.28), residues: 356 sheet: 0.42 (0.37), residues: 224 loop : -0.21 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 313 HIS 0.004 0.001 HIS B 179 PHE 0.009 0.001 PHE D 286 TYR 0.011 0.001 TYR B 314 ARG 0.014 0.001 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 440) hydrogen bonds : angle 5.53836 ( 1224) covalent geometry : bond 0.00422 (10180) covalent geometry : angle 0.54113 (13808) *********************** 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 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.191 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 68 average time/residue: 1.5037 time to fit residues: 109.4452 Evaluate side-chains 64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 244 ASP 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 79 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 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 = 0.2882 r_free = 0.2882 target = 0.045083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.036209 restraints weight = 31492.348| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 2.84 r_work: 0.2468 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2350 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9331 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10180 Z= 0.136 Angle : 0.510 7.186 13808 Z= 0.278 Chirality : 0.044 0.134 1572 Planarity : 0.005 0.065 1796 Dihedral : 4.045 18.621 1412 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.35 % Allowed : 13.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1316 helix: 1.90 (0.28), residues: 352 sheet: 0.46 (0.37), residues: 224 loop : -0.22 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 313 HIS 0.004 0.001 HIS B 179 PHE 0.007 0.001 PHE D 286 TYR 0.009 0.001 TYR B 314 ARG 0.015 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 440) hydrogen bonds : angle 5.43353 ( 1224) covalent geometry : bond 0.00311 (10180) covalent geometry : angle 0.51041 (13808) *********************** 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 70 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.217 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 67 average time/residue: 1.7177 time to fit residues: 123.1112 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 : 1.352 ------------------------------------------------------------------------------- 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 101 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 128 optimal weight: 0.0970 chunk 88 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** 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 = 0.2844 r_free = 0.2844 target = 0.043741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.034689 restraints weight = 32201.039| |-----------------------------------------------------------------------------| r_work (start): 0.2550 rms_B_bonded: 2.86 r_work: 0.2413 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2295 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9364 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 10180 Z= 0.244 Angle : 0.588 8.875 13808 Z= 0.321 Chirality : 0.047 0.155 1572 Planarity : 0.005 0.070 1796 Dihedral : 4.272 20.632 1412 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.96 % Allowed : 14.04 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.25), residues: 1316 helix: 1.73 (0.28), residues: 356 sheet: 0.38 (0.37), residues: 224 loop : -0.23 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 313 HIS 0.005 0.001 HIS B 179 PHE 0.010 0.001 PHE D 286 TYR 0.011 0.001 TYR B 314 ARG 0.017 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 440) hydrogen bonds : angle 5.62230 ( 1224) covalent geometry : bond 0.00568 (10180) covalent geometry : angle 0.58808 (13808) *********************** 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 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.269 Fit side-chains REVERT: A 113 GLN cc_start: 0.9185 (pm20) cc_final: 0.8968 (pm20) REVERT: B 113 GLN cc_start: 0.9190 (pm20) cc_final: 0.8973 (pm20) REVERT: D 113 GLN cc_start: 0.9185 (pm20) cc_final: 0.8969 (pm20) outliers start: 10 outliers final: 10 residues processed: 69 average time/residue: 1.9389 time to fit residues: 142.8111 Evaluate side-chains 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 244 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 120 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.035112 restraints weight = 31962.993| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 2.88 r_work: 0.2427 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2309 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9354 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 10180 Z= 0.202 Angle : 0.558 8.307 13808 Z= 0.303 Chirality : 0.046 0.137 1572 Planarity : 0.005 0.075 1796 Dihedral : 4.241 20.889 1412 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.96 % Allowed : 14.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1316 helix: 1.76 (0.28), residues: 356 sheet: 0.42 (0.37), residues: 224 loop : -0.22 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 313 HIS 0.004 0.001 HIS B 179 PHE 0.009 0.001 PHE D 286 TYR 0.011 0.001 TYR B 314 ARG 0.018 0.001 ARG C 80 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 440) hydrogen bonds : angle 5.54331 ( 1224) covalent geometry : bond 0.00469 (10180) covalent geometry : angle 0.55775 (13808) *********************** 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 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 1.338 Fit side-chains REVERT: A 113 GLN cc_start: 0.9188 (pm20) cc_final: 0.8970 (pm20) REVERT: B 113 GLN cc_start: 0.9191 (pm20) cc_final: 0.8971 (pm20) REVERT: D 113 GLN cc_start: 0.9187 (pm20) cc_final: 0.8970 (pm20) outliers start: 10 outliers final: 13 residues processed: 69 average time/residue: 1.6134 time to fit residues: 119.1215 Evaluate side-chains 72 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 195 LEU 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 244 ASP Chi-restraints excluded: chain D residue 316 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** 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 = 0.2865 r_free = 0.2865 target = 0.044574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.035569 restraints weight = 31829.484| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.87 r_work: 0.2439 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9342 moved from start: 0.2141 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= 0.158 Angle : 0.534 7.866 13808 Z= 0.289 Chirality : 0.045 0.130 1572 Planarity : 0.005 0.079 1796 Dihedral : 4.213 22.118 1412 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1316 helix: 1.89 (0.28), residues: 352 sheet: 0.47 (0.37), residues: 224 loop : -0.23 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 313 HIS 0.004 0.000 HIS B 179 PHE 0.008 0.001 PHE D 286 TYR 0.010 0.001 TYR B 314 ARG 0.019 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 440) hydrogen bonds : angle 5.44011 ( 1224) covalent geometry : bond 0.00365 (10180) covalent geometry : angle 0.53364 (13808) *********************** 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 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.177 Fit side-chains REVERT: A 113 GLN cc_start: 0.9182 (pm20) cc_final: 0.8969 (pm20) REVERT: B 113 GLN cc_start: 0.9179 (pm20) cc_final: 0.8967 (pm20) REVERT: D 113 GLN cc_start: 0.9177 (pm20) cc_final: 0.8966 (pm20) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 1.5963 time to fit residues: 110.7599 Evaluate side-chains 63 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 63 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 118 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.037791 restraints weight = 31553.829| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.87 r_work: 0.2516 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10180 Z= 0.087 Angle : 0.481 6.709 13808 Z= 0.258 Chirality : 0.043 0.128 1572 Planarity : 0.005 0.083 1796 Dihedral : 3.942 21.312 1412 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1316 helix: 2.05 (0.28), residues: 352 sheet: 0.56 (0.38), residues: 220 loop : -0.11 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 313 HIS 0.004 0.000 HIS D 179 PHE 0.005 0.001 PHE D 286 TYR 0.005 0.001 TYR B 314 ARG 0.019 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.02721 ( 440) hydrogen bonds : angle 5.10678 ( 1224) covalent geometry : bond 0.00193 (10180) covalent geometry : angle 0.48057 (13808) ********************** 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 69 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.089 Fit side-chains REVERT: A 113 GLN cc_start: 0.9153 (pm20) cc_final: 0.8953 (pm20) REVERT: D 113 GLN cc_start: 0.9152 (pm20) cc_final: 0.8952 (pm20) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 1.5149 time to fit residues: 111.7441 Evaluate side-chains 64 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 316 ASN 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 102 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 130 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.044111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.035062 restraints weight = 31723.850| |-----------------------------------------------------------------------------| r_work (start): 0.2561 rms_B_bonded: 2.86 r_work: 0.2425 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2306 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9355 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10180 Z= 0.203 Angle : 0.562 8.582 13808 Z= 0.305 Chirality : 0.046 0.159 1572 Planarity : 0.005 0.081 1796 Dihedral : 4.233 21.347 1412 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.77 % Allowed : 15.00 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.25), residues: 1316 helix: 1.83 (0.28), residues: 356 sheet: 0.39 (0.37), residues: 224 loop : -0.14 (0.26), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 313 HIS 0.006 0.001 HIS D 179 PHE 0.009 0.001 PHE B 286 TYR 0.011 0.001 TYR A 314 ARG 0.019 0.001 ARG D 80 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 440) hydrogen bonds : angle 5.45332 ( 1224) covalent geometry : bond 0.00475 (10180) covalent geometry : angle 0.56170 (13808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7902.74 seconds wall clock time: 138 minutes 36.98 seconds (8316.98 seconds total)