Starting phenix.real_space_refine on Wed Sep 25 07:55:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_29661.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_29661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_29661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_29661.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g14_29661/09_2024/8g14_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.90, per 1000 atoms: 0.49 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: 2.44 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: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.699A 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: 2.85 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.210 Find NCS groups from input model: 0.330 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.119 Fit side-chains outliers start: 12 outliers final: 16 residues processed: 88 average time/residue: 1.3638 time to fit residues: 128.7763 Evaluate side-chains 80 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 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 fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.191 Fit side-chains outliers start: 16 outliers final: 4 residues processed: 68 average time/residue: 1.4158 time to fit residues: 103.4103 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 66 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9243 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 10220 Z= 0.509 Angle : 0.619 9.092 13860 Z= 0.345 Chirality : 0.054 0.217 1580 Planarity : 0.005 0.051 1800 Dihedral : 7.883 118.051 1416 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.98 % Allowed : 14.25 % 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: 0.17 (0.24), residues: 1328 helix: 1.05 (0.27), residues: 368 sheet: -0.44 (0.34), residues: 256 loop : -0.08 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 313 HIS 0.004 0.001 HIS C 53 PHE 0.013 0.002 PHE B 286 TYR 0.015 0.002 TYR C 314 ARG 0.003 0.001 ARG D 200 *********************** 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 77 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 1.128 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 77 average time/residue: 1.2798 time to fit residues: 106.2748 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10220 Z= 0.140 Angle : 0.462 6.262 13860 Z= 0.257 Chirality : 0.046 0.142 1580 Planarity : 0.004 0.044 1800 Dihedral : 4.282 18.619 1408 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.28 % Allowed : 15.85 % Favored : 83.87 % 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: 1.49 (0.27), residues: 372 sheet: 0.02 (0.33), residues: 276 loop : -0.22 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS C 53 PHE 0.006 0.001 PHE D 295 TYR 0.009 0.001 TYR C 314 ARG 0.001 0.000 ARG A 234 *********************** 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 63 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.171 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 1.3687 time to fit residues: 92.9750 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10220 Z= 0.332 Angle : 0.532 7.658 13860 Z= 0.297 Chirality : 0.050 0.170 1580 Planarity : 0.004 0.048 1800 Dihedral : 4.490 16.619 1408 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.38 % Allowed : 16.51 % 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: 0.41 (0.24), residues: 1328 helix: 1.44 (0.27), residues: 372 sheet: -0.01 (0.33), residues: 276 loop : -0.18 (0.26), residues: 680 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 0.009 0.001 PHE C 286 TYR 0.012 0.001 TYR D 314 ARG 0.003 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 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.148 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 1.5251 time to fit residues: 98.1861 Evaluate side-chains 59 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 237 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 0.0050 chunk 42 optimal weight: 0.0980 chunk 67 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1173 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= 0.123 Angle : 0.441 5.923 13860 Z= 0.245 Chirality : 0.046 0.143 1580 Planarity : 0.004 0.043 1800 Dihedral : 4.153 18.426 1408 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.28 % Allowed : 16.70 % 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: 0.65 (0.24), residues: 1328 helix: 1.75 (0.27), residues: 372 sheet: 0.16 (0.33), residues: 276 loop : -0.12 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.001 0.000 HIS B 179 PHE 0.005 0.001 PHE A 295 TYR 0.008 0.001 TYR C 314 ARG 0.001 0.000 ARG B 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 63 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.067 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 63 average time/residue: 1.3867 time to fit residues: 94.0080 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10220 Z= 0.322 Angle : 0.524 7.382 13860 Z= 0.291 Chirality : 0.050 0.161 1580 Planarity : 0.004 0.047 1800 Dihedral : 4.439 16.292 1408 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.38 % Allowed : 16.89 % Favored : 82.74 % 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: 0.56 (0.24), residues: 1328 helix: 1.60 (0.26), residues: 372 sheet: 0.12 (0.33), residues: 276 loop : -0.14 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.003 0.001 HIS C 53 PHE 0.008 0.001 PHE C 286 TYR 0.012 0.001 TYR A 314 ARG 0.002 0.000 ARG A 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 64 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.061 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 64 average time/residue: 1.3003 time to fit residues: 89.7860 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 0.0010 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 111 optimal weight: 3.9990 overall best weight: 1.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1164 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= 0.144 Angle : 0.447 5.939 13860 Z= 0.247 Chirality : 0.046 0.144 1580 Planarity : 0.004 0.044 1800 Dihedral : 4.170 17.758 1408 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.09 % Allowed : 17.17 % Favored : 82.74 % 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: 0.73 (0.24), residues: 1328 helix: 1.87 (0.27), residues: 372 sheet: 0.22 (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 A 313 HIS 0.001 0.000 HIS C 53 PHE 0.006 0.001 PHE B 295 TYR 0.008 0.001 TYR B 314 ARG 0.001 0.000 ARG B 197 *********************** 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 61 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.060 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.4077 time to fit residues: 92.3927 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 10220 Z= 0.138 Angle : 0.441 5.776 13860 Z= 0.244 Chirality : 0.046 0.143 1580 Planarity : 0.004 0.043 1800 Dihedral : 4.094 16.829 1408 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % 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: 1.94 (0.27), residues: 372 sheet: 0.22 (0.33), residues: 276 loop : -0.05 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 313 HIS 0.001 0.000 HIS C 53 PHE 0.006 0.001 PHE A 295 TYR 0.008 0.001 TYR A 314 ARG 0.001 0.000 ARG A 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 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.5541 time to fit residues: 99.9893 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9226 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 10220 Z= 0.391 Angle : 0.556 8.030 13860 Z= 0.309 Chirality : 0.051 0.181 1580 Planarity : 0.004 0.049 1800 Dihedral : 4.498 15.844 1408 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.09 % Allowed : 17.17 % Favored : 82.74 % 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: 0.60 (0.24), residues: 1328 helix: 1.66 (0.26), residues: 372 sheet: 0.18 (0.33), residues: 276 loop : -0.15 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 313 HIS 0.003 0.001 HIS C 53 PHE 0.010 0.001 PHE D 286 TYR 0.013 0.002 TYR D 314 ARG 0.003 0.001 ARG A 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 fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.126 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.4034 time to fit residues: 92.2198 Evaluate side-chains 60 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.063966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.050490 restraints weight = 19072.533| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.44 r_work: 0.2482 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1180 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= 0.138 Angle : 0.446 5.778 13860 Z= 0.247 Chirality : 0.046 0.144 1580 Planarity : 0.003 0.042 1800 Dihedral : 4.149 18.315 1408 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % 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: 0.79 (0.25), residues: 1328 helix: 1.98 (0.27), residues: 372 sheet: 0.27 (0.34), residues: 276 loop : -0.13 (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 53 PHE 0.006 0.001 PHE C 295 TYR 0.008 0.001 TYR A 314 ARG 0.001 0.000 ARG B 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.00 seconds wall clock time: 49 minutes 31.76 seconds (2971.76 seconds total)