Starting phenix.real_space_refine on Wed Feb 4 06:01:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.map" model { file = "/net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j99_61256/02_2026/9j99_61256.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 24 5.16 5 C 5866 2.51 5 N 1302 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8859 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2466 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "C" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 341 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 292 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "E" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 325 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 4, 'TRANS': 35} Chain: "I" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2469 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "K" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 341 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 292 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "M" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 348 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 4, 'TRANS': 38} Chain: "A" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 319 Unusual residues: {'PC1': 7, 'UND': 5} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-1': 1, 'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'PC1': 2, 'UND': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'UND': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 135 Unusual residues: {'PC1': 3, 'UND': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'PC1': 1, 'UND': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "I" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 394 Unusual residues: {'PC1': 8, 'UND': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 93 Chain: "J" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 77 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'PC1': 1, 'UND': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 71 Unusual residues: {'PC1': 1, 'UND': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 1.75, per 1000 atoms: 0.20 Number of scatterers: 8859 At special positions: 0 Unit cell: (138.7, 100.7, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 25 15.00 O 1642 8.00 N 1302 7.00 C 5866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 264.2 milliseconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 34.8% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'B' and resid 88 through 135 removed outlier: 3.695A pdb=" N LYS B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.678A pdb=" N ASP B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 49 removed outlier: 3.565A pdb=" N ARG C 15 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.823A pdb=" N GLU D 29 " --> pdb=" O GLN D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 29' Processing helix chain 'D' and resid 30 through 50 removed outlier: 4.427A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.522A pdb=" N ALA D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.620A pdb=" N VAL E 27 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA E 28 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N HIS E 29 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 30 " --> pdb=" O VAL E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 30' Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 49 through 54 Processing helix chain 'I' and resid 51 through 56 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 Processing helix chain 'I' and resid 375 through 379 removed outlier: 4.047A pdb=" N GLY I 378 " --> pdb=" O ASP I 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 135 removed outlier: 3.676A pdb=" N THR J 101 " --> pdb=" O ASN J 97 " (cutoff:3.500A) Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 11 through 49 removed outlier: 3.791A pdb=" N ARG K 15 " --> pdb=" O GLU K 11 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 51 removed outlier: 4.080A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 57 Processing helix chain 'M' and resid 19 through 24 Processing helix chain 'M' and resid 27 through 30 removed outlier: 3.608A pdb=" N TYR M 30 " --> pdb=" O VAL M 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 27 through 30' Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.598A pdb=" N PHE M 35 " --> pdb=" O GLY M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 91 removed outlier: 6.741A pdb=" N ASN A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 350 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 91 removed outlier: 3.582A pdb=" N LEU I 125 " --> pdb=" O ASN I 122 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU I 336 " --> pdb=" O VAL I 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP I 350 " --> pdb=" O ASP I 345 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1387 1.32 - 1.44: 2207 1.44 - 1.57: 5287 1.57 - 1.69: 50 1.69 - 1.81: 40 Bond restraints: 8971 Sorted by residual: bond pdb=" N VAL I 198 " pdb=" CA VAL I 198 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.04e+01 bond pdb=" N VAL I 196 " pdb=" CA VAL I 196 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.89e+00 bond pdb=" N GLY A 299 " pdb=" CA GLY A 299 " ideal model delta sigma weight residual 1.451 1.483 -0.032 1.06e-02 8.90e+03 9.15e+00 bond pdb=" N LEU E 54 " pdb=" CA LEU E 54 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.26e-02 6.30e+03 7.77e+00 bond pdb=" N VAL A 297 " pdb=" CA VAL A 297 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.29e-02 6.01e+03 7.57e+00 ... (remaining 8966 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 11724 2.59 - 5.18: 163 5.18 - 7.78: 28 7.78 - 10.37: 1 10.37 - 12.96: 1 Bond angle restraints: 11917 Sorted by residual: angle pdb=" N SER K 38 " pdb=" CA SER K 38 " pdb=" C SER K 38 " ideal model delta sigma weight residual 109.81 122.77 -12.96 2.21e+00 2.05e-01 3.44e+01 angle pdb=" C ASP A 134 " pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta sigma weight residual 110.35 120.15 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" N ASN A 133 " pdb=" CA ASN A 133 " pdb=" C ASN A 133 " ideal model delta sigma weight residual 110.48 103.07 7.41 1.48e+00 4.57e-01 2.51e+01 angle pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 121.47 115.93 5.54 1.15e+00 7.56e-01 2.32e+01 angle pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 112.60 117.41 -4.81 1.00e+00 1.00e+00 2.32e+01 ... (remaining 11912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4894 17.90 - 35.80: 482 35.80 - 53.69: 174 53.69 - 71.59: 42 71.59 - 89.49: 9 Dihedral angle restraints: 5601 sinusoidal: 2779 harmonic: 2822 Sorted by residual: dihedral pdb=" C ASP A 134 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta harmonic sigma weight residual -122.60 -137.49 14.89 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" N ASP A 134 " pdb=" C ASP A 134 " pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta harmonic sigma weight residual 122.80 134.74 -11.94 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" CA PRO E 58 " pdb=" C PRO E 58 " pdb=" N SER E 59 " pdb=" CA SER E 59 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 5598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1114 0.090 - 0.179: 96 0.179 - 0.269: 4 0.269 - 0.358: 0 0.358 - 0.448: 1 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CA ASP A 134 " pdb=" N ASP A 134 " pdb=" C ASP A 134 " pdb=" CB ASP A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA SER K 38 " pdb=" N SER K 38 " pdb=" C SER K 38 " pdb=" CB SER K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLU A 298 " pdb=" N GLU A 298 " pdb=" C GLU A 298 " pdb=" CB GLU A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1212 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 207 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 95 " -0.045 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO I 96 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO I 96 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 96 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 33 " 0.042 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO M 34 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO M 34 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 34 " 0.035 5.00e-02 4.00e+02 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2585 2.84 - 3.36: 6535 3.36 - 3.87: 12453 3.87 - 4.39: 14562 4.39 - 4.90: 27652 Nonbonded interactions: 63787 Sorted by model distance: nonbonded pdb=" CG HIS A 346 " pdb=" NE2 HIS A 346 " model vdw 2.329 2.672 nonbonded pdb=" O PHE D 27 " pdb=" OG SER D 30 " model vdw 2.352 3.040 nonbonded pdb=" O ASP B 131 " pdb=" OG SER B 134 " model vdw 2.360 3.040 nonbonded pdb=" O ASP I 73 " pdb=" NH1 ARG I 315 " model vdw 2.361 3.120 nonbonded pdb=" OG SER I 312 " pdb=" OG SER J 116 " model vdw 2.361 3.040 ... (remaining 63782 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' and (resid 49 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O )) or resid 181 through 343 or (resid 344 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CD1)) or resid 345 through 350 \ or (resid 351 and (name N or name CA or name C or name O or name CB or name CG2 \ )) or resid 352 through 367 or (resid 368 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD2)) or resid 369 through 382 or resid 402 o \ r (resid 403 and (name N or name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or na \ me C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name C2B o \ r name C2C or name C2D or name C2E or name C2F or name C2G or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or nam \ e C38 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )) or (resid 405 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C3 or nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C3A or name O11 or name O12 or name O13 or name O1 \ 4 or name O21 or name O31 or name O32 or name P )) or (resid 407 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or \ (resid 409 and (name N or name C1 or name C11 or name C12 or name C13 or name C \ 14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 or nam \ e C25 or name C26 or name C27 or name O11 or name O12 or name O13 or name O14 or \ name O21 or name O22 or name P )))) selection = (chain 'I' and (resid 49 through 280 or resid 294 through 345 or (resid 346 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CE1 or name NE2)) or resid 347 through 382 or resid 402 or (resid 403 and (name \ N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ e C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or \ name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or name C2D \ or name C2E or name C2F or name C2G or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )) or (resid 405 and (name N or name C1 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C2 or name C3 or name C31 or name C32 or n \ ame C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 \ or name C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name \ O31 or name O32 or name P )) or resid 407 or (resid 409 and (name N or name C1 o \ r name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C2 \ 1 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name P )))) \ } ncs_group { reference = (chain 'B' and (resid 87 through 135 or resid 202)) selection = (chain 'J' and (resid 87 through 135 or (resid 202 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C3 or name C31 or name C32 or name O11 or name O12 or name O13 or name \ O14 or name O21 or name O22 or name O31 or name O32 or name P )))) } ncs_group { reference = (chain 'C' and resid 10 through 49) selection = chain 'K' } ncs_group { reference = (chain 'D' and resid 24 through 61) selection = (chain 'L' and resid 24 through 61) } ncs_group { reference = (chain 'E' and (resid 21 through 101 or resid 104)) selection = (chain 'M' and (resid 21 through 101 or resid 104)) } 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: 2.160 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8971 Z= 0.276 Angle : 0.778 12.962 11917 Z= 0.422 Chirality : 0.053 0.448 1215 Planarity : 0.007 0.084 1406 Dihedral : 16.627 89.489 3775 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.00 % Allowed : 7.52 % Favored : 88.48 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 956 helix: 0.21 (0.25), residues: 302 sheet: 0.16 (0.27), residues: 410 loop : -1.11 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 85 TYR 0.013 0.002 TYR I 307 PHE 0.017 0.002 PHE I 176 TRP 0.013 0.002 TRP A 243 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 8971) covalent geometry : angle 0.77773 (11917) hydrogen bonds : bond 0.17725 ( 516) hydrogen bonds : angle 7.11939 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.218 Fit side-chains REVERT: A 85 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8073 (ttt180) REVERT: A 111 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9065 (mt) REVERT: A 183 LEU cc_start: 0.8408 (tp) cc_final: 0.8135 (mp) REVERT: B 97 ASN cc_start: 0.8757 (m-40) cc_final: 0.8455 (m-40) REVERT: B 126 MET cc_start: 0.7870 (ttm) cc_final: 0.7651 (ttm) REVERT: D 28 LYS cc_start: 0.7469 (tttt) cc_final: 0.7002 (mtpm) REVERT: I 85 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8236 (ttt180) REVERT: I 164 MET cc_start: 0.8430 (mtp) cc_final: 0.8053 (mtm) REVERT: I 192 GLU cc_start: 0.8021 (mp0) cc_final: 0.7565 (mp0) REVERT: I 206 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8258 (p) REVERT: I 298 GLU cc_start: 0.7754 (tt0) cc_final: 0.7012 (pp20) REVERT: I 374 LEU cc_start: 0.7707 (mt) cc_final: 0.7150 (tt) REVERT: J 126 MET cc_start: 0.7707 (ttm) cc_final: 0.7087 (tmm) outliers start: 33 outliers final: 2 residues processed: 159 average time/residue: 0.5989 time to fit residues: 101.2401 Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 65 ASN A 130 ASN A 311 GLN A 371 GLN D 50 GLN E 46 ASN I 65 ASN I 109 GLN I 349 ASN J 121 GLN J 122 GLN K 17 HIS M 46 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108300 restraints weight = 9320.294| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.39 r_work: 0.3087 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8971 Z= 0.130 Angle : 0.559 9.224 11917 Z= 0.281 Chirality : 0.039 0.160 1215 Planarity : 0.005 0.062 1406 Dihedral : 16.452 87.301 2032 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.30 % Allowed : 14.55 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 956 helix: 2.25 (0.29), residues: 296 sheet: 0.47 (0.25), residues: 432 loop : -0.71 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.013 0.001 PHE I 359 TRP 0.009 0.001 TRP M 41 HIS 0.003 0.001 HIS I 102 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8971) covalent geometry : angle 0.55893 (11917) hydrogen bonds : bond 0.04413 ( 516) hydrogen bonds : angle 4.76677 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.322 Fit side-chains REVERT: A 192 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7159 (pp20) REVERT: A 272 GLU cc_start: 0.8538 (tt0) cc_final: 0.8189 (tt0) REVERT: A 279 MET cc_start: 0.7373 (tpp) cc_final: 0.7157 (mmm) REVERT: A 302 THR cc_start: 0.9122 (t) cc_final: 0.8869 (m) REVERT: D 28 LYS cc_start: 0.7565 (tttt) cc_final: 0.7043 (mtpm) REVERT: D 50 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8865 (mm110) REVERT: I 170 ASP cc_start: 0.8440 (t0) cc_final: 0.8228 (t70) REVERT: I 192 GLU cc_start: 0.8134 (mp0) cc_final: 0.7628 (mp0) REVERT: I 298 GLU cc_start: 0.7757 (tt0) cc_final: 0.6957 (pp20) REVERT: I 330 ARG cc_start: 0.8780 (tpt90) cc_final: 0.8536 (mmm160) REVERT: I 374 LEU cc_start: 0.7628 (mt) cc_final: 0.7068 (tt) REVERT: J 126 MET cc_start: 0.7682 (ttm) cc_final: 0.7154 (tmm) outliers start: 19 outliers final: 4 residues processed: 110 average time/residue: 0.6329 time to fit residues: 73.7112 Evaluate side-chains 87 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 17 HIS E 46 ASN I 109 GLN J 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105126 restraints weight = 9278.976| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.32 r_work: 0.3041 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8971 Z= 0.221 Angle : 0.639 9.575 11917 Z= 0.320 Chirality : 0.042 0.170 1215 Planarity : 0.005 0.057 1406 Dihedral : 16.845 88.471 2020 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.36 % Allowed : 14.30 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.28), residues: 956 helix: 2.58 (0.30), residues: 302 sheet: 0.74 (0.26), residues: 423 loop : -0.64 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 330 TYR 0.012 0.002 TYR I 307 PHE 0.013 0.001 PHE I 104 TRP 0.012 0.002 TRP A 243 HIS 0.004 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 8971) covalent geometry : angle 0.63912 (11917) hydrogen bonds : bond 0.05265 ( 516) hydrogen bonds : angle 4.69674 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.230 Fit side-chains REVERT: A 192 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7147 (pp20) REVERT: A 279 MET cc_start: 0.7470 (tpp) cc_final: 0.7194 (mmm) REVERT: B 97 ASN cc_start: 0.8873 (m-40) cc_final: 0.8600 (m-40) REVERT: D 28 LYS cc_start: 0.7460 (tttt) cc_final: 0.6938 (mtpm) REVERT: E 54 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8882 (mt) REVERT: E 55 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8795 (p) REVERT: I 181 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8755 (ptpp) REVERT: I 192 GLU cc_start: 0.8256 (mp0) cc_final: 0.7618 (mp0) REVERT: I 240 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (mttm) REVERT: I 298 GLU cc_start: 0.7967 (tt0) cc_final: 0.7059 (pp20) REVERT: I 374 LEU cc_start: 0.7521 (mt) cc_final: 0.6941 (tt) REVERT: J 126 MET cc_start: 0.7696 (ttm) cc_final: 0.7108 (tmm) REVERT: M 23 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8103 (mp) outliers start: 36 outliers final: 14 residues processed: 107 average time/residue: 0.5996 time to fit residues: 68.2242 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 240 LYS Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain M residue 23 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 46 ASN E 52 ASN I 109 GLN J 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106463 restraints weight = 9394.645| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.39 r_work: 0.3059 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8971 Z= 0.153 Angle : 0.573 9.178 11917 Z= 0.284 Chirality : 0.040 0.162 1215 Planarity : 0.005 0.054 1406 Dihedral : 16.378 87.251 2020 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.52 % Allowed : 15.64 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.28), residues: 956 helix: 3.02 (0.29), residues: 296 sheet: 0.82 (0.25), residues: 423 loop : -0.46 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.010 0.001 TYR I 307 PHE 0.011 0.001 PHE I 104 TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8971) covalent geometry : angle 0.57281 (11917) hydrogen bonds : bond 0.04273 ( 516) hydrogen bonds : angle 4.45198 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.273 Fit side-chains REVERT: A 85 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7934 (ttt180) REVERT: A 192 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7342 (pp20) REVERT: A 279 MET cc_start: 0.7521 (tpp) cc_final: 0.7254 (mmm) REVERT: A 343 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: D 28 LYS cc_start: 0.7612 (tttt) cc_final: 0.7109 (mtpm) REVERT: D 50 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8816 (mm110) REVERT: I 192 GLU cc_start: 0.8142 (mp0) cc_final: 0.7554 (mp0) REVERT: I 298 GLU cc_start: 0.7701 (tt0) cc_final: 0.6919 (pp20) REVERT: I 374 LEU cc_start: 0.7677 (mt) cc_final: 0.7090 (tt) REVERT: J 126 MET cc_start: 0.7611 (ttm) cc_final: 0.7074 (tmm) outliers start: 29 outliers final: 12 residues processed: 103 average time/residue: 0.5814 time to fit residues: 63.5364 Evaluate side-chains 89 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 46 ASN I 109 GLN J 122 GLN L 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107994 restraints weight = 9541.021| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.23 r_work: 0.3119 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8971 Z= 0.108 Angle : 0.525 8.614 11917 Z= 0.259 Chirality : 0.038 0.151 1215 Planarity : 0.004 0.053 1406 Dihedral : 15.921 87.200 2020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.91 % Allowed : 16.00 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 956 helix: 3.32 (0.29), residues: 296 sheet: 0.86 (0.24), residues: 430 loop : -0.39 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.009 0.001 PHE I 104 TRP 0.009 0.001 TRP A 243 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8971) covalent geometry : angle 0.52508 (11917) hydrogen bonds : bond 0.03520 ( 516) hydrogen bonds : angle 4.23771 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.322 Fit side-chains REVERT: A 85 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8115 (ttt180) REVERT: A 192 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7389 (pp20) REVERT: A 272 GLU cc_start: 0.8850 (tt0) cc_final: 0.8631 (tt0) REVERT: A 279 MET cc_start: 0.7503 (tpp) cc_final: 0.7235 (mmm) REVERT: A 302 THR cc_start: 0.9190 (t) cc_final: 0.8985 (m) REVERT: A 343 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: A 360 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8315 (tt0) REVERT: D 28 LYS cc_start: 0.7587 (tttt) cc_final: 0.7080 (mtpm) REVERT: I 192 GLU cc_start: 0.8302 (mp0) cc_final: 0.7665 (mp0) REVERT: I 298 GLU cc_start: 0.7867 (tt0) cc_final: 0.7115 (pp20) REVERT: I 330 ARG cc_start: 0.8804 (tpt90) cc_final: 0.8531 (mmm160) REVERT: I 374 LEU cc_start: 0.7693 (mt) cc_final: 0.7082 (tt) REVERT: J 126 MET cc_start: 0.7670 (ttm) cc_final: 0.7098 (tmm) outliers start: 24 outliers final: 8 residues processed: 104 average time/residue: 0.6205 time to fit residues: 68.4669 Evaluate side-chains 92 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 206 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN E 46 ASN I 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.105979 restraints weight = 9518.171| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.23 r_work: 0.3085 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8971 Z= 0.157 Angle : 0.575 8.856 11917 Z= 0.283 Chirality : 0.040 0.157 1215 Planarity : 0.004 0.052 1406 Dihedral : 16.128 87.008 2020 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.27 % Allowed : 16.12 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.27), residues: 956 helix: 3.37 (0.29), residues: 296 sheet: 0.91 (0.24), residues: 423 loop : -0.31 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 330 TYR 0.009 0.001 TYR I 307 PHE 0.011 0.001 PHE I 104 TRP 0.010 0.001 TRP A 243 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8971) covalent geometry : angle 0.57455 (11917) hydrogen bonds : bond 0.04204 ( 516) hydrogen bonds : angle 4.35141 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.335 Fit side-chains REVERT: A 85 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8139 (ttt180) REVERT: A 192 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7425 (pp20) REVERT: A 279 MET cc_start: 0.7521 (tpp) cc_final: 0.7254 (mmm) REVERT: A 343 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: A 360 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: D 28 LYS cc_start: 0.7641 (tttt) cc_final: 0.7137 (mtpm) REVERT: I 88 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8643 (mt) REVERT: I 192 GLU cc_start: 0.8283 (mp0) cc_final: 0.7632 (mp0) REVERT: I 298 GLU cc_start: 0.7915 (tt0) cc_final: 0.7086 (pp20) REVERT: I 374 LEU cc_start: 0.7688 (mt) cc_final: 0.7064 (tt) REVERT: J 126 MET cc_start: 0.7694 (ttm) cc_final: 0.7133 (tmm) outliers start: 27 outliers final: 13 residues processed: 106 average time/residue: 0.6270 time to fit residues: 70.7404 Evaluate side-chains 97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN D 50 GLN E 46 ASN I 89 ASN I 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108427 restraints weight = 9513.327| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.22 r_work: 0.3142 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8971 Z= 0.115 Angle : 0.535 8.384 11917 Z= 0.262 Chirality : 0.038 0.154 1215 Planarity : 0.004 0.053 1406 Dihedral : 15.748 87.121 2020 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.03 % Allowed : 16.61 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.28), residues: 956 helix: 3.52 (0.29), residues: 296 sheet: 0.97 (0.24), residues: 429 loop : -0.30 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.011 0.001 PHE M 50 TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8971) covalent geometry : angle 0.53531 (11917) hydrogen bonds : bond 0.03534 ( 516) hydrogen bonds : angle 4.19025 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.344 Fit side-chains REVERT: A 85 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: A 192 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7439 (pp20) REVERT: A 279 MET cc_start: 0.7501 (tpp) cc_final: 0.7242 (mmm) REVERT: A 343 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: A 360 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8308 (tt0) REVERT: D 28 LYS cc_start: 0.7569 (tttt) cc_final: 0.7056 (mtpm) REVERT: D 50 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8855 (mm110) REVERT: I 192 GLU cc_start: 0.8278 (mp0) cc_final: 0.7672 (mp0) REVERT: I 298 GLU cc_start: 0.7875 (tt0) cc_final: 0.7081 (pp20) REVERT: I 330 ARG cc_start: 0.8794 (tpt90) cc_final: 0.8523 (mmm160) REVERT: I 374 LEU cc_start: 0.7737 (mt) cc_final: 0.7112 (tt) REVERT: J 126 MET cc_start: 0.7748 (ttm) cc_final: 0.7223 (tmm) outliers start: 25 outliers final: 10 residues processed: 102 average time/residue: 0.6345 time to fit residues: 68.7899 Evaluate side-chains 92 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.0060 chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN D 50 GLN E 46 ASN I 89 ASN I 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109708 restraints weight = 9509.551| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.13 r_work: 0.3201 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8971 Z= 0.081 Angle : 0.492 8.344 11917 Z= 0.238 Chirality : 0.037 0.150 1215 Planarity : 0.004 0.053 1406 Dihedral : 15.095 87.528 2020 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.82 % Allowed : 17.45 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.28), residues: 956 helix: 3.71 (0.29), residues: 296 sheet: 1.16 (0.24), residues: 427 loop : -0.26 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.005 0.000 TYR I 307 PHE 0.012 0.001 PHE M 50 TRP 0.010 0.001 TRP M 41 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00170 ( 8971) covalent geometry : angle 0.49241 (11917) hydrogen bonds : bond 0.02576 ( 516) hydrogen bonds : angle 3.89355 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.326 Fit side-chains REVERT: A 85 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8150 (ttt180) REVERT: A 133 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7549 (p0) REVERT: A 192 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7456 (pp20) REVERT: A 279 MET cc_start: 0.7434 (tpp) cc_final: 0.7208 (mmm) REVERT: A 343 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8413 (tm-30) REVERT: D 28 LYS cc_start: 0.7642 (tttt) cc_final: 0.7105 (mtpm) REVERT: D 50 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8884 (mm110) REVERT: I 192 GLU cc_start: 0.8245 (mp0) cc_final: 0.7770 (mp0) REVERT: I 298 GLU cc_start: 0.7875 (tt0) cc_final: 0.7171 (pp20) REVERT: I 330 ARG cc_start: 0.8792 (tpt90) cc_final: 0.8554 (mmm160) REVERT: I 374 LEU cc_start: 0.7799 (mt) cc_final: 0.7191 (tt) REVERT: J 126 MET cc_start: 0.7706 (ttm) cc_final: 0.7149 (tmm) outliers start: 15 outliers final: 4 residues processed: 112 average time/residue: 0.6381 time to fit residues: 75.7452 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain I residue 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 121 GLN E 46 ASN I 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110443 restraints weight = 9341.293| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.07 r_work: 0.3120 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8971 Z= 0.123 Angle : 0.557 8.051 11917 Z= 0.272 Chirality : 0.039 0.168 1215 Planarity : 0.004 0.051 1406 Dihedral : 15.307 86.686 2020 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.06 % Allowed : 17.70 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.27), residues: 956 helix: 3.79 (0.28), residues: 294 sheet: 1.18 (0.24), residues: 428 loop : -0.20 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.010 0.001 PHE M 50 TRP 0.009 0.001 TRP A 243 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8971) covalent geometry : angle 0.55738 (11917) hydrogen bonds : bond 0.03476 ( 516) hydrogen bonds : angle 4.04234 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.325 Fit side-chains REVERT: A 85 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8147 (ttt180) REVERT: A 192 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7417 (pp20) REVERT: A 279 MET cc_start: 0.7433 (tpp) cc_final: 0.7198 (mmm) REVERT: A 360 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: A 372 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7943 (mt0) REVERT: D 28 LYS cc_start: 0.7524 (tttt) cc_final: 0.6987 (mtpm) REVERT: I 164 MET cc_start: 0.8449 (mtp) cc_final: 0.8204 (mtm) REVERT: I 192 GLU cc_start: 0.8238 (mp0) cc_final: 0.7627 (mp0) REVERT: I 298 GLU cc_start: 0.7895 (tt0) cc_final: 0.7096 (pp20) REVERT: I 330 ARG cc_start: 0.8814 (tpt90) cc_final: 0.8539 (mmm160) REVERT: I 374 LEU cc_start: 0.7664 (mt) cc_final: 0.7052 (tt) REVERT: J 126 MET cc_start: 0.7701 (ttm) cc_final: 0.7104 (tmm) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.6704 time to fit residues: 71.5744 Evaluate side-chains 93 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 43 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN E 46 ASN I 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106389 restraints weight = 9480.440| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.13 r_work: 0.3114 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8971 Z= 0.114 Angle : 0.560 8.310 11917 Z= 0.271 Chirality : 0.038 0.158 1215 Planarity : 0.004 0.052 1406 Dihedral : 15.239 86.992 2020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 18.06 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.27), residues: 956 helix: 3.79 (0.28), residues: 294 sheet: 1.12 (0.24), residues: 431 loop : -0.12 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.010 0.001 PHE M 50 TRP 0.009 0.001 TRP M 41 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8971) covalent geometry : angle 0.55987 (11917) hydrogen bonds : bond 0.03341 ( 516) hydrogen bonds : angle 4.02516 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.309 Fit side-chains REVERT: A 85 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8166 (ttt180) REVERT: A 192 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7443 (pp20) REVERT: A 279 MET cc_start: 0.7427 (tpp) cc_final: 0.7199 (mmm) REVERT: A 372 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7965 (mt0) REVERT: D 28 LYS cc_start: 0.7571 (tttt) cc_final: 0.7065 (mtpm) REVERT: I 164 MET cc_start: 0.8440 (mtp) cc_final: 0.8211 (mtm) REVERT: I 192 GLU cc_start: 0.8259 (mp0) cc_final: 0.7660 (mp0) REVERT: I 298 GLU cc_start: 0.7910 (tt0) cc_final: 0.7121 (pp20) REVERT: I 330 ARG cc_start: 0.8816 (tpt90) cc_final: 0.8541 (mmm160) REVERT: I 374 LEU cc_start: 0.7704 (mt) cc_final: 0.7090 (tt) REVERT: J 126 MET cc_start: 0.7714 (ttm) cc_final: 0.7138 (tmm) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 0.6321 time to fit residues: 64.2445 Evaluate side-chains 96 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 127 GLU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain K residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN D 50 GLN E 46 ASN I 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106418 restraints weight = 9439.683| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.12 r_work: 0.3112 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8971 Z= 0.115 Angle : 0.562 9.261 11917 Z= 0.274 Chirality : 0.039 0.162 1215 Planarity : 0.004 0.052 1406 Dihedral : 15.190 87.058 2020 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.18 % Allowed : 17.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.27), residues: 956 helix: 3.82 (0.28), residues: 294 sheet: 1.12 (0.24), residues: 432 loop : -0.10 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 330 TYR 0.008 0.001 TYR I 307 PHE 0.010 0.001 PHE M 50 TRP 0.009 0.001 TRP A 243 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8971) covalent geometry : angle 0.56192 (11917) hydrogen bonds : bond 0.03372 ( 516) hydrogen bonds : angle 4.03047 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3092.83 seconds wall clock time: 53 minutes 25.47 seconds (3205.47 seconds total)