Starting phenix.real_space_refine on Fri Feb 14 06:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.map" model { file = "/net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g14_29661/02_2025/8g14_29661.cif" } resolution = 2.3 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= 0.001 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 6332 2.51 5 N 1728 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10020 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2505 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: C, B, D Time building chain proxies: 4.81, per 1000 atoms: 0.48 Number of scatterers: 10020 At special positions: 0 Unit cell: (96.025, 101.035, 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 1912 8.00 N 1728 7.00 C 6332 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 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: 56 helices and 8 sheets defined 39.2% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 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: 3.699A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.626A 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 113 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.503A 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 195 through 200 Processing helix chain 'A' and resid 212 through 221 removed outlier: 3.907A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 removed outlier: 3.522A pdb=" N ASN A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) No H-bonds generated for '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: 3.527A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.581A pdb=" N SER A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) 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: 3.699A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.626A 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 113 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.503A 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 195 through 200 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.907A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 removed outlier: 3.522A pdb=" N ASN B 225 " --> pdb=" O PRO B 222 " (cutoff:3.500A) No H-bonds generated for '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: 3.527A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.581A pdb=" N SER B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) 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: 3.700A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.626A 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 113 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.503A 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 195 through 200 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.907A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 removed outlier: 3.522A pdb=" N ASN C 225 " --> pdb=" O PRO C 222 " (cutoff:3.500A) No H-bonds generated for '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: 3.527A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 335 removed outlier: 3.581A pdb=" N SER C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 335 " --> pdb=" O MET C 331 " (cutoff:3.500A) 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: 3.699A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.626A 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 113 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.503A 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 195 through 200 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.907A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 removed outlier: 3.522A pdb=" N ASN D 225 " --> pdb=" O PRO D 222 " (cutoff:3.500A) No H-bonds generated for '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: 3.527A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.581A pdb=" N SER D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU D 335 " --> pdb=" O MET D 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.200A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.715A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.726A 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: 10.200A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.715A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N PHE B 307 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N GLY B 300 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N LYS B 309 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLY B 298 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.726A 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: 10.200A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 210 removed outlier: 3.715A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.726A 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: 10.200A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 207 through 210 removed outlier: 3.715A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.281A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.882A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1248 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: 3.19 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3000 1.34 - 1.45: 1534 1.45 - 1.57: 5602 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10220 Sorted by residual: bond pdb=" N ILE D 207 " pdb=" CA ILE D 207 " ideal model delta sigma weight residual 1.461 1.494 -0.034 9.10e-03 1.21e+04 1.36e+01 bond pdb=" N ILE C 207 " pdb=" CA ILE C 207 " ideal model delta sigma weight residual 1.461 1.493 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" N ILE A 207 " pdb=" CA ILE A 207 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.10e-03 1.21e+04 1.26e+01 bond pdb=" N ILE B 207 " pdb=" CA ILE B 207 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.10e-03 1.21e+04 1.26e+01 bond pdb=" N ASN B 205 " pdb=" CA ASN B 205 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.27e-02 6.20e+03 7.49e+00 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13180 1.42 - 2.84: 539 2.84 - 4.26: 97 4.26 - 5.68: 27 5.68 - 7.10: 17 Bond angle restraints: 13860 Sorted by residual: angle pdb=" C ILE A 206 " pdb=" N ILE A 207 " pdb=" CA ILE A 207 " ideal model delta sigma weight residual 123.02 118.09 4.93 1.04e+00 9.25e-01 2.24e+01 angle pdb=" C ILE C 206 " pdb=" N ILE C 207 " pdb=" CA ILE C 207 " ideal model delta sigma weight residual 123.02 118.11 4.91 1.04e+00 9.25e-01 2.23e+01 angle pdb=" C ILE B 206 " pdb=" N ILE B 207 " pdb=" CA ILE B 207 " ideal model delta sigma weight residual 123.02 118.11 4.91 1.04e+00 9.25e-01 2.23e+01 angle pdb=" C ILE D 206 " pdb=" N ILE D 207 " pdb=" CA ILE D 207 " ideal model delta sigma weight residual 123.02 118.12 4.90 1.04e+00 9.25e-01 2.22e+01 angle pdb=" N ASN A 239 " pdb=" CA ASN A 239 " pdb=" C ASN A 239 " ideal model delta sigma weight residual 110.80 117.80 -7.00 2.13e+00 2.20e-01 1.08e+01 ... (remaining 13855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5336 17.41 - 34.81: 508 34.81 - 52.22: 160 52.22 - 69.63: 24 69.63 - 87.03: 12 Dihedral angle restraints: 6040 sinusoidal: 2264 harmonic: 3776 Sorted by residual: dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA B 238 " pdb=" C ALA B 238 " pdb=" N ASN B 239 " pdb=" CA ASN B 239 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ALA D 238 " pdb=" C ALA D 238 " pdb=" N ASN D 239 " pdb=" CA ASN D 239 " ideal model delta harmonic sigma weight residual 180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1165 0.054 - 0.107: 299 0.107 - 0.161: 112 0.161 - 0.215: 0 0.215 - 0.268: 4 Chirality restraints: 1580 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 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE D 206 " pdb=" N ILE D 206 " pdb=" C ILE D 206 " pdb=" CB ILE D 206 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 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 2.70 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1577 not shown) Planarity restraints: 1800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 244 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" CG ASP C 244 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP C 244 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 244 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 244 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" CG ASP A 244 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP A 244 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 244 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 244 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" CG ASP D 244 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP D 244 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP D 244 " 0.012 2.00e-02 2.50e+03 ... (remaining 1797 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3779 2.90 - 3.40: 8808 3.40 - 3.90: 16490 3.90 - 4.40: 19454 4.40 - 4.90: 33052 Nonbonded interactions: 81583 Sorted by model distance: nonbonded pdb=" N ASP B 127 " pdb=" OD1 ASP B 127 " model vdw 2.404 3.120 nonbonded pdb=" N ASP C 127 " pdb=" OD1 ASP C 127 " model vdw 2.404 3.120 nonbonded pdb=" N ASP D 127 " pdb=" OD1 ASP D 127 " model vdw 2.404 3.120 nonbonded pdb=" N ASP A 127 " pdb=" OD1 ASP A 127 " model vdw 2.405 3.120 nonbonded pdb=" OE2 GLU D 97 " pdb=" OG1 THR D 99 " model vdw 2.409 3.040 ... (remaining 81578 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: 0.08 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: 1.050 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.630 Find NCS groups from input model: 0.240 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9165 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 : 0.005 0.040 10220 Z= 0.296 Angle : 0.720 7.100 13860 Z= 0.430 Chirality : 0.056 0.268 1580 Planarity : 0.006 0.050 1800 Dihedral : 15.717 87.035 3632 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.13 % Allowed : 15.75 % Favored : 83.11 % 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: -1.00 (0.22), residues: 1328 helix: -0.88 (0.23), residues: 360 sheet: -0.03 (0.38), residues: 220 loop : -0.68 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 87 HIS 0.003 0.001 HIS A 53 PHE 0.009 0.001 PHE D 295 TYR 0.017 0.002 TYR B 314 ARG 0.006 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.157 Fit side-chains outliers start: 12 outliers final: 16 residues processed: 88 average time/residue: 1.4243 time to fit residues: 134.1860 Evaluate side-chains 80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 335 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.2883 r_free = 0.2883 target = 0.061577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.048369 restraints weight = 19229.183| |-----------------------------------------------------------------------------| r_work (start): 0.2576 rms_B_bonded: 2.37 r_work: 0.2442 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10220 Z= 0.293 Angle : 0.537 7.787 13860 Z= 0.301 Chirality : 0.049 0.174 1580 Planarity : 0.005 0.051 1800 Dihedral : 7.596 103.433 1436 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.51 % Allowed : 15.09 % Favored : 83.40 % 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: 0.09 (0.24), residues: 1328 helix: 0.91 (0.27), residues: 368 sheet: -0.11 (0.35), residues: 276 loop : -0.24 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 313 HIS 0.003 0.001 HIS D 53 PHE 0.008 0.001 PHE D 286 TYR 0.012 0.001 TYR A 314 ARG 0.003 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 1.124 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 68 average time/residue: 1.5214 time to fit residues: 110.6596 Evaluate side-chains 60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 244 ASP Chi-restraints excluded: chain D residue 244 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 101 optimal weight: 0.0020 chunk 12 optimal weight: 0.0570 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1510 ------------------------------------------------------------------------------- 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 = 0.2922 r_free = 0.2922 target = 0.063679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.050456 restraints weight = 19380.829| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.42 r_work: 0.2493 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2376 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10220 Z= 0.141 Angle : 0.453 6.130 13860 Z= 0.253 Chirality : 0.046 0.138 1580 Planarity : 0.004 0.042 1800 Dihedral : 7.430 115.289 1416 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.66 % Allowed : 15.57 % Favored : 83.77 % 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: 0.30 (0.24), residues: 1328 helix: 1.36 (0.28), residues: 372 sheet: -0.32 (0.33), residues: 288 loop : -0.13 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 313 HIS 0.002 0.000 HIS C 53 PHE 0.005 0.001 PHE C 295 TYR 0.009 0.001 TYR C 314 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.289 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 67 average time/residue: 1.4153 time to fit residues: 102.1006 Evaluate side-chains 60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.2900 r_free = 0.2900 target = 0.062951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.049401 restraints weight = 19413.814| |-----------------------------------------------------------------------------| r_work (start): 0.2592 rms_B_bonded: 2.43 r_work: 0.2458 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2338 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10220 Z= 0.194 Angle : 0.475 6.586 13860 Z= 0.264 Chirality : 0.047 0.141 1580 Planarity : 0.004 0.045 1800 Dihedral : 4.214 17.533 1408 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.85 % Allowed : 15.75 % Favored : 83.40 % 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: 0.42 (0.24), residues: 1328 helix: 1.50 (0.27), residues: 372 sheet: -0.30 (0.32), residues: 288 loop : -0.05 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 313 HIS 0.002 0.000 HIS C 53 PHE 0.007 0.001 PHE A 295 TYR 0.011 0.001 TYR C 314 ARG 0.002 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.168 Fit side-chains REVERT: A 86 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8945 (mmmm) REVERT: B 86 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (mmmm) REVERT: C 86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8949 (mmmm) REVERT: D 86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8947 (mmmm) outliers start: 9 outliers final: 0 residues processed: 69 average time/residue: 1.5115 time to fit residues: 111.9745 Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain D residue 86 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 96 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- 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 = 0.2884 r_free = 0.2884 target = 0.062097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.048442 restraints weight = 19318.355| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 2.42 r_work: 0.2438 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2316 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 10220 Z= 0.246 Angle : 0.496 7.061 13860 Z= 0.276 Chirality : 0.048 0.148 1580 Planarity : 0.004 0.046 1800 Dihedral : 4.307 17.130 1408 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.75 % Allowed : 16.13 % Favored : 83.11 % 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: 0.50 (0.24), residues: 1328 helix: 1.56 (0.28), residues: 368 sheet: -0.06 (0.33), residues: 276 loop : -0.10 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.002 0.001 HIS C 53 PHE 0.007 0.001 PHE D 286 TYR 0.012 0.001 TYR C 314 ARG 0.002 0.000 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 1.160 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 68 average time/residue: 1.3781 time to fit residues: 101.1395 Evaluate side-chains 60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 0.0970 chunk 118 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.2913 r_free = 0.2913 target = 0.063568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.050030 restraints weight = 19364.629| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.44 r_work: 0.2473 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2353 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10220 Z= 0.157 Angle : 0.452 6.112 13860 Z= 0.251 Chirality : 0.047 0.141 1580 Planarity : 0.004 0.043 1800 Dihedral : 4.143 18.088 1408 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.38 % Allowed : 16.60 % Favored : 83.02 % 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: 0.61 (0.24), residues: 1328 helix: 1.70 (0.27), residues: 372 sheet: 0.04 (0.33), residues: 276 loop : -0.09 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.002 0.000 HIS C 53 PHE 0.006 0.001 PHE C 295 TYR 0.009 0.001 TYR A 314 ARG 0.001 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.055 Fit side-chains REVERT: A 86 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8941 (mmmm) REVERT: B 86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8947 (mmmm) REVERT: C 86 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8946 (mmmm) REVERT: D 86 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8945 (mmmm) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.6346 time to fit residues: 111.8990 Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain D residue 86 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.2868 r_free = 0.2868 target = 0.061384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.047649 restraints weight = 19636.642| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 2.45 r_work: 0.2415 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2294 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 10220 Z= 0.316 Angle : 0.524 7.529 13860 Z= 0.291 Chirality : 0.050 0.162 1580 Planarity : 0.004 0.047 1800 Dihedral : 4.391 16.598 1408 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.28 % Allowed : 16.79 % Favored : 82.92 % 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: 0.57 (0.24), residues: 1328 helix: 1.59 (0.27), residues: 368 sheet: 0.08 (0.33), residues: 276 loop : -0.08 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.003 0.001 HIS C 53 PHE 0.008 0.001 PHE D 286 TYR 0.013 0.001 TYR A 314 ARG 0.003 0.000 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.167 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 1.4506 time to fit residues: 98.2733 Evaluate side-chains 60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.062361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.048775 restraints weight = 19430.450| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 2.43 r_work: 0.2440 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10220 Z= 0.222 Angle : 0.486 6.846 13860 Z= 0.269 Chirality : 0.048 0.145 1580 Planarity : 0.004 0.046 1800 Dihedral : 4.293 17.614 1408 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.38 % Allowed : 16.98 % Favored : 82.64 % 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: 0.65 (0.24), residues: 1328 helix: 1.74 (0.27), residues: 372 sheet: 0.17 (0.33), residues: 276 loop : -0.11 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.002 0.000 HIS C 53 PHE 0.007 0.001 PHE C 295 TYR 0.011 0.001 TYR B 314 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.129 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.5140 time to fit residues: 104.7115 Evaluate side-chains 60 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.2919 r_free = 0.2919 target = 0.063888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.050345 restraints weight = 19323.988| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.45 r_work: 0.2481 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10220 Z= 0.141 Angle : 0.445 5.852 13860 Z= 0.246 Chirality : 0.046 0.143 1580 Planarity : 0.003 0.043 1800 Dihedral : 4.103 17.893 1408 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.38 % Allowed : 16.98 % Favored : 82.64 % 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: 0.77 (0.24), residues: 1328 helix: 1.89 (0.27), residues: 372 sheet: 0.23 (0.33), residues: 276 loop : -0.07 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.001 0.000 HIS C 179 PHE 0.006 0.001 PHE C 295 TYR 0.009 0.001 TYR A 314 ARG 0.001 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.219 Fit side-chains REVERT: A 86 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8927 (mmmm) REVERT: B 86 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8926 (mmmm) REVERT: C 86 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8928 (mmmm) REVERT: D 86 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8938 (mmmm) outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.5759 time to fit residues: 108.1315 Evaluate side-chains 64 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain D residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 123 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 = 0.2875 r_free = 0.2875 target = 0.061779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.048163 restraints weight = 19438.538| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 2.43 r_work: 0.2424 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10220 Z= 0.290 Angle : 0.513 7.320 13860 Z= 0.284 Chirality : 0.049 0.156 1580 Planarity : 0.004 0.046 1800 Dihedral : 4.341 16.654 1408 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.09 % Allowed : 17.26 % Favored : 82.64 % 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 (0.24), residues: 1328 helix: 1.75 (0.27), residues: 368 sheet: 0.24 (0.34), residues: 276 loop : -0.08 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.002 0.001 HIS D 53 PHE 0.008 0.001 PHE D 286 TYR 0.012 0.001 TYR A 314 ARG 0.002 0.000 ARG C 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.093 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 1.4899 time to fit residues: 97.6321 Evaluate side-chains 61 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.2934 r_free = 0.2934 target = 0.064649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.051144 restraints weight = 19330.996| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.45 r_work: 0.2501 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 10220 Z= 0.110 Angle : 0.432 5.498 13860 Z= 0.239 Chirality : 0.046 0.141 1580 Planarity : 0.003 0.042 1800 Dihedral : 4.034 18.278 1408 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.28 % Allowed : 17.08 % Favored : 82.64 % 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: 0.81 (0.25), residues: 1328 helix: 1.96 (0.27), residues: 372 sheet: 0.11 (0.33), residues: 288 loop : 0.00 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 313 HIS 0.001 0.000 HIS B 53 PHE 0.005 0.001 PHE A 295 TYR 0.007 0.001 TYR A 314 ARG 0.001 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6557.29 seconds wall clock time: 117 minutes 5.80 seconds (7025.80 seconds total)