Starting phenix.real_space_refine on Thu Jun 4 03:24:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.map" model { file = "/net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkr_74382/06_2026/9zkr_74382.cif" } resolution = 3.08 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= 0.030 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 7 5.49 5 S 65 5.16 5 C 6712 2.51 5 N 1476 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9928 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1029 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1027 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1033 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1047 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1084 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1326 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'OLC': 2, 'PLM': 4, 'POV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'OLC': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 172 Unusual residues: {'OLC': 2, 'PLM': 3, 'POV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 105 Unusual residues: {'OLC': 2, 'PLM': 2, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.46, per 1000 atoms: 0.25 Number of scatterers: 9928 At special positions: 0 Unit cell: (114.675, 117.975, 84.975, 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 65 16.00 P 7 15.00 O 1668 8.00 N 1476 7.00 C 6712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 91 " distance=2.02 Simple disulfide: pdb=" SG CYS G 90 " - pdb=" SG CYS G 100 " distance=2.04 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 91 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 100 " distance=2.04 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: 1.14 Conformation dependent library (CDL) restraints added in 405.3 milliseconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 75.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 623 Processing helix chain 'A' and resid 788 through 813 removed outlier: 3.644A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.508A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 623 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.691A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.537A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.728A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 38 removed outlier: 3.762A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 85 removed outlier: 5.119A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 106 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 127 through 159 removed outlier: 3.700A pdb=" N ALA E 140 " --> pdb=" O TRP E 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 28 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 4.303A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 3.866A pdb=" N SER F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 210 removed outlier: 3.827A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 40 removed outlier: 3.859A pdb=" N VAL G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 128 through 150 removed outlier: 3.780A pdb=" N VAL G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 183 Processing helix chain 'G' and resid 202 through 234 removed outlier: 3.556A pdb=" N HIS G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 40 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 151 Processing helix chain 'H' and resid 155 through 184 removed outlier: 3.649A pdb=" N GLY H 162 " --> pdb=" O ILE H 158 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 178 " --> pdb=" O ILE H 174 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 184 " --> pdb=" O ILE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 removed outlier: 3.741A pdb=" N TYR H 206 " --> pdb=" O GLY H 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 7.252A pdb=" N LEU G 81 " --> pdb=" O LEU G 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 48 Processing sheet with id=AA4, first strand: chain 'H' and resid 88 through 89 741 hydrogen bonds defined for protein. 2187 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: 1.63 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1774 1.33 - 1.46: 3128 1.46 - 1.59: 5119 1.59 - 1.71: 14 1.71 - 1.84: 91 Bond restraints: 10126 Sorted by residual: bond pdb=" O12 POV A1004 " pdb=" P POV A1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" O12 POV C1004 " pdb=" P POV C1004 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" O12 POV D1003 " pdb=" P POV D1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.56e+00 bond pdb=" O12 POV H 501 " pdb=" P POV H 501 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" O12 POV C1003 " pdb=" P POV C1003 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.45e+00 ... (remaining 10121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 13283 2.72 - 5.44: 247 5.44 - 8.15: 29 8.15 - 10.87: 5 10.87 - 13.59: 1 Bond angle restraints: 13565 Sorted by residual: angle pdb=" N ILE D 573 " pdb=" CA ILE D 573 " pdb=" C ILE D 573 " ideal model delta sigma weight residual 111.81 107.79 4.02 8.60e-01 1.35e+00 2.19e+01 angle pdb=" CA LEU D 808 " pdb=" CB LEU D 808 " pdb=" CG LEU D 808 " ideal model delta sigma weight residual 116.30 129.89 -13.59 3.50e+00 8.16e-02 1.51e+01 angle pdb=" CB GLU E 134 " pdb=" CG GLU E 134 " pdb=" CD GLU E 134 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.70e+00 3.46e-01 1.26e+01 angle pdb=" CA LYS F 129 " pdb=" CB LYS F 129 " pdb=" CG LYS F 129 " ideal model delta sigma weight residual 114.10 120.86 -6.76 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CB MET E 123 " pdb=" CG MET E 123 " pdb=" SD MET E 123 " ideal model delta sigma weight residual 112.70 122.83 -10.13 3.00e+00 1.11e-01 1.14e+01 ... (remaining 13560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 5712 35.21 - 70.41: 128 70.41 - 105.62: 11 105.62 - 140.83: 20 140.83 - 176.03: 5 Dihedral angle restraints: 5876 sinusoidal: 2444 harmonic: 3432 Sorted by residual: dihedral pdb=" CB CYS H 52 " pdb=" SG CYS H 52 " pdb=" SG CYS H 91 " pdb=" CB CYS H 91 " ideal model delta sinusoidal sigma weight residual -86.00 -39.48 -46.52 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CA CYS H 100 " pdb=" C CYS H 100 " pdb=" N VAL H 101 " pdb=" CA VAL H 101 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CB CYS F 67 " pdb=" SG CYS F 67 " pdb=" SG CYS F 77 " pdb=" CB CYS F 77 " ideal model delta sinusoidal sigma weight residual -86.00 -43.18 -42.82 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 5873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1326 0.068 - 0.135: 175 0.135 - 0.203: 11 0.203 - 0.271: 2 0.271 - 0.338: 3 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CA GLU E 134 " pdb=" N GLU E 134 " pdb=" C GLU E 134 " pdb=" CB GLU E 134 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CB VAL H 101 " pdb=" CA VAL H 101 " pdb=" CG1 VAL H 101 " pdb=" CG2 VAL H 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL F 28 " pdb=" CA VAL F 28 " pdb=" CG1 VAL F 28 " pdb=" CG2 VAL F 28 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1514 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 519 " -0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO B 520 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 520 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 520 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.98e+00 pdb=" N PRO D 520 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 515 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO C 516 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.037 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1771 2.77 - 3.30: 9714 3.30 - 3.83: 16567 3.83 - 4.37: 19007 4.37 - 4.90: 33349 Nonbonded interactions: 80408 Sorted by model distance: nonbonded pdb=" O ILE F 134 " pdb=" OG SER F 137 " model vdw 2.233 3.040 nonbonded pdb=" O PRO A 516 " pdb=" ND2 ASN A 615 " model vdw 2.274 3.120 nonbonded pdb=" OG1 THR H 47 " pdb=" ND2 ASN H 197 " model vdw 2.285 3.120 nonbonded pdb=" O LEU E 16 " pdb=" OG SER E 19 " model vdw 2.300 3.040 nonbonded pdb=" O ILE F 140 " pdb=" OG SER F 144 " model vdw 2.305 3.040 ... (remaining 80403 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 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 781 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 585 or resid 587 through 628 or resid 785 through 799 o \ r resid 801 through 817)) selection = (chain 'C' and (resid 507 through 543 or (resid 565 and (name N or name CA or na \ me C or name O or name CB )) or resid 566 through 581 or resid 583 through 624 o \ r resid 781 through 795 or resid 797 through 811 or (resid 812 through 813 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 585 or resid 587 through 628 or resid 785 through 799 o \ r resid 801 through 817)) } ncs_group { reference = (chain 'G' and (resid 15 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 501)) selection = (chain 'H' and (resid 15 through 106 or resid 115 through 153 or (resid 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 185 or \ resid 197 through 230 or (resid 231 and (name N or name CA or name C or name O \ or name CB )) or resid 232 through 501)) } 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: 4.030 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.950 Find NCS groups from input model: 0.180 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 0.051 10132 Z= 0.276 Angle : 0.868 13.591 13577 Z= 0.434 Chirality : 0.048 0.338 1517 Planarity : 0.006 0.077 1591 Dihedral : 17.981 176.033 3656 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.59 % 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: 1.11 (0.24), residues: 1149 helix: 1.46 (0.17), residues: 895 sheet: -1.75 (1.26), residues: 10 loop : -1.87 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 37 TYR 0.033 0.002 TYR H 199 PHE 0.026 0.002 PHE E 23 TRP 0.044 0.002 TRP F 178 HIS 0.010 0.002 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.28 (10126) covalent geometry : angle 0.86608 / 0.43 (13565) SS BOND : bond 0.00691 / 0.35 ( 6) SS BOND : angle 2.16450 / 1.26 ( 12) hydrogen bonds : bond 0.12601 / 8.15 ( 741) hydrogen bonds : angle 5.26650 / 3.76 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.384 Fit side-chains REVERT: A 566 GLU cc_start: 0.6597 (tp30) cc_final: 0.5916 (tp30) REVERT: A 625 MET cc_start: 0.8287 (mtp) cc_final: 0.8035 (mtt) REVERT: B 586 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7710 (mmt90) REVERT: C 619 PHE cc_start: 0.7573 (m-80) cc_final: 0.7159 (m-80) REVERT: C 804 LEU cc_start: 0.7086 (tp) cc_final: 0.6821 (tt) REVERT: D 594 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7578 (mtp85) REVERT: E 87 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6879 (mm-30) REVERT: E 99 PHE cc_start: 0.6700 (m-10) cc_final: 0.6304 (m-10) REVERT: E 123 MET cc_start: 0.5809 (mmm) cc_final: 0.4236 (pmm) REVERT: E 132 GLN cc_start: 0.6538 (mm-40) cc_final: 0.6001 (tp-100) REVERT: F 125 SER cc_start: 0.7807 (t) cc_final: 0.7529 (p) REVERT: F 127 PHE cc_start: 0.6329 (t80) cc_final: 0.6037 (t80) REVERT: F 196 LEU cc_start: 0.8394 (mm) cc_final: 0.8087 (mm) REVERT: G 34 LEU cc_start: 0.7383 (mp) cc_final: 0.7169 (mt) REVERT: G 42 ASP cc_start: 0.5710 (t0) cc_final: 0.5468 (t0) REVERT: G 90 CYS cc_start: 0.5017 (t) cc_final: 0.4498 (t) REVERT: G 96 LYS cc_start: 0.5897 (mttp) cc_final: 0.5166 (tppt) REVERT: H 48 ARG cc_start: 0.7069 (ttm110) cc_final: 0.5427 (ttp80) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1040 time to fit residues: 30.9217 Evaluate side-chains 173 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.0070 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 ASN F 132 HIS F 199 HIS F 207 GLN H 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.179639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134547 restraints weight = 11934.951| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.96 r_work: 0.3358 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10132 Z= 0.152 Angle : 0.574 9.833 13577 Z= 0.296 Chirality : 0.039 0.195 1517 Planarity : 0.004 0.073 1591 Dihedral : 15.963 160.720 1772 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 8.73 % Favored : 89.32 % 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: 2.39 (0.25), residues: 1149 helix: 2.45 (0.17), residues: 895 sheet: -0.88 (1.66), residues: 10 loop : -1.79 (0.35), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 229 TYR 0.024 0.001 TYR G 226 PHE 0.030 0.002 PHE A 542 TRP 0.019 0.001 TRP F 178 HIS 0.008 0.001 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10126) covalent geometry : angle 0.57219 / 0.30 (13565) SS BOND : bond 0.00719 / 0.35 ( 6) SS BOND : angle 1.51692 / 0.95 ( 12) hydrogen bonds : bond 0.04383 / 2.93 ( 741) hydrogen bonds : angle 3.76132 / 2.72 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.412 Fit side-chains REVERT: A 566 GLU cc_start: 0.7132 (tp30) cc_final: 0.6670 (tp30) REVERT: B 586 ARG cc_start: 0.8784 (mtp85) cc_final: 0.8333 (mmt90) REVERT: C 804 LEU cc_start: 0.8133 (tp) cc_final: 0.7845 (tt) REVERT: D 594 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8021 (mtp85) REVERT: E 99 PHE cc_start: 0.6984 (m-10) cc_final: 0.6615 (m-10) REVERT: E 123 MET cc_start: 0.6116 (mmm) cc_final: 0.4540 (pmm) REVERT: F 58 MET cc_start: 0.7635 (mmp) cc_final: 0.7405 (mmp) REVERT: F 99 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7634 (mtp180) REVERT: G 90 CYS cc_start: 0.5677 (t) cc_final: 0.5366 (t) REVERT: G 96 LYS cc_start: 0.6093 (mttp) cc_final: 0.5212 (tppt) REVERT: G 122 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: H 48 ARG cc_start: 0.7409 (ttm110) cc_final: 0.5532 (ttp80) REVERT: H 149 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6503 (mtp-110) outliers start: 19 outliers final: 10 residues processed: 205 average time/residue: 0.1065 time to fit residues: 30.0487 Evaluate side-chains 187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 787 ASN F 199 HIS F 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.177104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130739 restraints weight = 11977.496| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.69 r_work: 0.3293 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10132 Z= 0.158 Angle : 0.555 9.405 13577 Z= 0.287 Chirality : 0.038 0.210 1517 Planarity : 0.004 0.069 1591 Dihedral : 15.095 139.817 1772 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.36 % Allowed : 11.50 % Favored : 86.14 % 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: 2.60 (0.25), residues: 1149 helix: 2.60 (0.17), residues: 895 sheet: -4.38 (0.80), residues: 5 loop : -1.65 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.033 0.002 TYR G 226 PHE 0.036 0.001 PHE A 542 TRP 0.023 0.001 TRP F 178 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (10126) covalent geometry : angle 0.55382 / 0.29 (13565) SS BOND : bond 0.00702 / 0.34 ( 6) SS BOND : angle 1.34614 / 0.84 ( 12) hydrogen bonds : bond 0.04349 / 2.92 ( 741) hydrogen bonds : angle 3.67750 / 2.67 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.410 Fit side-chains REVERT: A 566 GLU cc_start: 0.7432 (tp30) cc_final: 0.7044 (tp30) REVERT: C 804 LEU cc_start: 0.8683 (tp) cc_final: 0.8457 (tt) REVERT: D 594 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8010 (mtp85) REVERT: E 64 LEU cc_start: 0.7745 (mp) cc_final: 0.7511 (pp) REVERT: E 65 ARG cc_start: 0.6637 (mtt180) cc_final: 0.6420 (mtt180) REVERT: E 87 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 99 PHE cc_start: 0.7187 (m-10) cc_final: 0.6865 (m-10) REVERT: E 123 MET cc_start: 0.6124 (mmm) cc_final: 0.4659 (pmm) REVERT: E 134 GLU cc_start: 0.6141 (OUTLIER) cc_final: 0.5794 (tp30) REVERT: F 99 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7680 (mtp180) REVERT: G 20 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: G 96 LYS cc_start: 0.6518 (mttp) cc_final: 0.5520 (tppt) REVERT: H 48 ARG cc_start: 0.7618 (ttm110) cc_final: 0.5644 (ttt-90) REVERT: H 149 ARG cc_start: 0.6822 (mtp180) cc_final: 0.6410 (mtp-110) outliers start: 23 outliers final: 13 residues processed: 192 average time/residue: 0.1063 time to fit residues: 28.3044 Evaluate side-chains 185 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS F 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128888 restraints weight = 12185.992| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.15 r_work: 0.3298 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10132 Z= 0.185 Angle : 0.578 9.149 13577 Z= 0.296 Chirality : 0.040 0.225 1517 Planarity : 0.004 0.065 1591 Dihedral : 15.095 137.442 1772 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.77 % Allowed : 14.27 % Favored : 82.96 % 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: 2.57 (0.25), residues: 1149 helix: 2.57 (0.17), residues: 895 sheet: -1.36 (1.42), residues: 15 loop : -1.66 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 204 TYR 0.030 0.002 TYR G 226 PHE 0.035 0.002 PHE A 542 TRP 0.012 0.001 TRP F 178 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (10126) covalent geometry : angle 0.57617 / 0.30 (13565) SS BOND : bond 0.00413 / 0.21 ( 6) SS BOND : angle 1.47709 / 0.88 ( 12) hydrogen bonds : bond 0.04427 / 2.97 ( 741) hydrogen bonds : angle 3.73401 / 2.71 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.382 Fit side-chains REVERT: A 566 GLU cc_start: 0.7205 (tp30) cc_final: 0.6745 (tp30) REVERT: C 804 LEU cc_start: 0.8261 (tp) cc_final: 0.7991 (tt) REVERT: D 545 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: D 594 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8048 (mtp85) REVERT: E 99 PHE cc_start: 0.7073 (m-10) cc_final: 0.6740 (m-10) REVERT: E 123 MET cc_start: 0.6139 (mmm) cc_final: 0.4481 (pmm) REVERT: E 134 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5756 (mm-30) REVERT: F 99 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7619 (mtp180) REVERT: G 20 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: G 96 LYS cc_start: 0.6250 (mttp) cc_final: 0.5317 (tppt) REVERT: G 122 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: H 48 ARG cc_start: 0.7647 (ttm110) cc_final: 0.5408 (ttt-90) outliers start: 27 outliers final: 16 residues processed: 192 average time/residue: 0.1092 time to fit residues: 28.5854 Evaluate side-chains 183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 103 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 787 ASN E 27 HIS F 199 HIS F 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133581 restraints weight = 11962.848| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.90 r_work: 0.3303 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10132 Z= 0.133 Angle : 0.520 9.332 13577 Z= 0.270 Chirality : 0.037 0.169 1517 Planarity : 0.004 0.061 1591 Dihedral : 14.077 123.786 1772 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.46 % Allowed : 15.61 % Favored : 81.93 % 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: 2.94 (0.25), residues: 1149 helix: 2.84 (0.17), residues: 896 sheet: -1.16 (1.40), residues: 15 loop : -1.58 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.016 0.001 TYR G 226 PHE 0.036 0.001 PHE A 542 TRP 0.010 0.001 TRP F 178 HIS 0.003 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10126) covalent geometry : angle 0.51883 / 0.27 (13565) SS BOND : bond 0.00244 / 0.13 ( 6) SS BOND : angle 1.15197 / 0.68 ( 12) hydrogen bonds : bond 0.04096 / 2.75 ( 741) hydrogen bonds : angle 3.56227 / 2.60 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.241 Fit side-chains REVERT: A 541 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8009 (mmm-85) REVERT: A 566 GLU cc_start: 0.7260 (tp30) cc_final: 0.6896 (tp30) REVERT: C 804 LEU cc_start: 0.8532 (tp) cc_final: 0.8316 (tt) REVERT: D 545 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: D 594 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7989 (mtp85) REVERT: E 64 LEU cc_start: 0.7708 (mp) cc_final: 0.7405 (pp) REVERT: E 65 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6216 (mtt-85) REVERT: E 87 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 99 PHE cc_start: 0.7201 (m-10) cc_final: 0.6807 (m-10) REVERT: E 123 MET cc_start: 0.6104 (mmm) cc_final: 0.4678 (pmm) REVERT: E 134 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5730 (tp30) REVERT: F 99 ARG cc_start: 0.7903 (mtp-110) cc_final: 0.7702 (mtp180) REVERT: G 20 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7549 (mp10) REVERT: G 96 LYS cc_start: 0.6460 (mttp) cc_final: 0.5463 (tppt) REVERT: G 122 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7591 (mmm-85) REVERT: H 48 ARG cc_start: 0.7769 (ttm110) cc_final: 0.5497 (ttt-90) outliers start: 24 outliers final: 16 residues processed: 183 average time/residue: 0.1016 time to fit residues: 25.6231 Evaluate side-chains 179 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain H residue 103 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS F 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.175192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128755 restraints weight = 12078.614| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.69 r_work: 0.3283 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10132 Z= 0.164 Angle : 0.549 8.912 13577 Z= 0.285 Chirality : 0.039 0.237 1517 Planarity : 0.004 0.059 1591 Dihedral : 14.148 116.160 1772 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.87 % Allowed : 16.74 % Favored : 80.39 % 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: 2.86 (0.25), residues: 1149 helix: 2.79 (0.16), residues: 892 sheet: -2.08 (1.17), residues: 20 loop : -1.46 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.017 0.001 TYR G 226 PHE 0.037 0.001 PHE A 542 TRP 0.009 0.001 TRP F 178 HIS 0.004 0.001 HIS G 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10126) covalent geometry : angle 0.54781 / 0.28 (13565) SS BOND : bond 0.00263 / 0.13 ( 6) SS BOND : angle 1.33984 / 0.81 ( 12) hydrogen bonds : bond 0.04314 / 2.91 ( 741) hydrogen bonds : angle 3.63430 / 2.65 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7382 (tp30) cc_final: 0.6994 (tp30) REVERT: D 545 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: D 594 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7951 (mtp85) REVERT: E 64 LEU cc_start: 0.7733 (mp) cc_final: 0.7320 (pp) REVERT: E 65 ARG cc_start: 0.6615 (mtt180) cc_final: 0.6331 (mtt-85) REVERT: E 99 PHE cc_start: 0.7212 (m-10) cc_final: 0.6854 (m-10) REVERT: E 123 MET cc_start: 0.6051 (mmm) cc_final: 0.4565 (pmm) REVERT: E 134 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5716 (tp30) REVERT: G 96 LYS cc_start: 0.6611 (mttp) cc_final: 0.5579 (tppt) REVERT: G 122 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7700 (mmm-85) REVERT: G 227 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7671 (mp) REVERT: H 48 ARG cc_start: 0.7848 (ttm110) cc_final: 0.5644 (ttt-90) REVERT: H 149 ARG cc_start: 0.6977 (mtp85) cc_final: 0.6587 (mtp-110) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.1125 time to fit residues: 28.8141 Evaluate side-chains 190 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN C 787 ASN E 27 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS G 234 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.178726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134711 restraints weight = 11942.548| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.87 r_work: 0.3322 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10132 Z= 0.122 Angle : 0.513 9.936 13577 Z= 0.267 Chirality : 0.038 0.201 1517 Planarity : 0.003 0.059 1591 Dihedral : 13.191 108.073 1772 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.36 % Allowed : 17.35 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.25), residues: 1149 helix: 2.97 (0.17), residues: 894 sheet: -2.15 (1.17), residues: 20 loop : -1.48 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.014 0.001 TYR G 226 PHE 0.035 0.001 PHE A 542 TRP 0.008 0.001 TRP C 574 HIS 0.005 0.001 HIS G 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10126) covalent geometry : angle 0.51241 / 0.27 (13565) SS BOND : bond 0.00199 / 0.10 ( 6) SS BOND : angle 1.02372 / 0.59 ( 12) hydrogen bonds : bond 0.03989 / 2.68 ( 741) hydrogen bonds : angle 3.50901 / 2.56 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7194 (tp30) cc_final: 0.6872 (tp30) REVERT: D 594 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7916 (mtp85) REVERT: E 82 PHE cc_start: 0.7354 (m-80) cc_final: 0.7104 (m-80) REVERT: E 87 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6952 (mm-30) REVERT: E 99 PHE cc_start: 0.7177 (m-10) cc_final: 0.6800 (m-10) REVERT: E 123 MET cc_start: 0.6056 (mmm) cc_final: 0.4520 (pmm) REVERT: G 96 LYS cc_start: 0.6539 (mttp) cc_final: 0.5529 (tppt) REVERT: G 122 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7644 (mmm-85) REVERT: G 227 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7470 (mp) REVERT: H 48 ARG cc_start: 0.7724 (ttm110) cc_final: 0.5454 (ttt-90) REVERT: H 149 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6718 (mtp-110) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 0.1088 time to fit residues: 27.5207 Evaluate side-chains 184 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 227 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN E 27 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS G 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.130807 restraints weight = 12087.718| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.71 r_work: 0.3303 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10132 Z= 0.139 Angle : 0.535 10.267 13577 Z= 0.276 Chirality : 0.038 0.192 1517 Planarity : 0.003 0.058 1591 Dihedral : 13.113 103.273 1772 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.16 % Allowed : 17.86 % Favored : 79.98 % 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: 3.09 (0.25), residues: 1149 helix: 2.95 (0.17), residues: 893 sheet: -2.12 (1.17), residues: 20 loop : -1.40 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.014 0.001 TYR G 151 PHE 0.036 0.001 PHE A 542 TRP 0.007 0.001 TRP F 178 HIS 0.006 0.001 HIS G 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10126) covalent geometry : angle 0.53402 / 0.28 (13565) SS BOND : bond 0.00273 / 0.14 ( 6) SS BOND : angle 1.11985 / 0.65 ( 12) hydrogen bonds : bond 0.04097 / 2.76 ( 741) hydrogen bonds : angle 3.55857 / 2.60 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7242 (tp30) cc_final: 0.6920 (tp30) REVERT: D 594 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7915 (mtp85) REVERT: E 82 PHE cc_start: 0.7390 (m-80) cc_final: 0.7126 (m-80) REVERT: E 87 GLU cc_start: 0.7434 (mm-30) cc_final: 0.6988 (mm-30) REVERT: E 99 PHE cc_start: 0.7205 (m-10) cc_final: 0.6935 (m-10) REVERT: G 20 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: G 96 LYS cc_start: 0.6646 (mttp) cc_final: 0.5634 (tppt) REVERT: G 122 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7694 (mmm-85) REVERT: G 227 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7528 (mp) REVERT: H 48 ARG cc_start: 0.7773 (ttm110) cc_final: 0.5524 (ttt-90) REVERT: H 88 ARG cc_start: 0.6889 (mtm180) cc_final: 0.6602 (mpp-170) REVERT: H 149 ARG cc_start: 0.6949 (mtp85) cc_final: 0.6679 (mtp-110) outliers start: 21 outliers final: 17 residues processed: 182 average time/residue: 0.1144 time to fit residues: 28.3568 Evaluate side-chains 186 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain D residue 788 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN E 27 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS G 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.179010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132655 restraints weight = 12016.820| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.73 r_work: 0.3333 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10132 Z= 0.121 Angle : 0.518 10.409 13577 Z= 0.268 Chirality : 0.038 0.227 1517 Planarity : 0.003 0.057 1591 Dihedral : 12.548 99.598 1772 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.05 % Allowed : 18.07 % Favored : 79.88 % 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: 3.21 (0.25), residues: 1149 helix: 3.04 (0.17), residues: 894 sheet: -2.09 (1.18), residues: 20 loop : -1.36 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 586 TYR 0.015 0.001 TYR G 226 PHE 0.035 0.001 PHE A 542 TRP 0.008 0.001 TRP C 574 HIS 0.007 0.001 HIS G 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10126) covalent geometry : angle 0.51765 / 0.27 (13565) SS BOND : bond 0.00194 / 0.10 ( 6) SS BOND : angle 0.95711 / 0.55 ( 12) hydrogen bonds : bond 0.03916 / 2.64 ( 741) hydrogen bonds : angle 3.47583 / 2.54 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7231 (tp30) cc_final: 0.6962 (tp30) REVERT: D 594 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7871 (mtp85) REVERT: E 82 PHE cc_start: 0.7279 (m-80) cc_final: 0.7026 (m-80) REVERT: E 87 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6928 (mm-30) REVERT: E 99 PHE cc_start: 0.7169 (m-10) cc_final: 0.6881 (m-10) REVERT: E 123 MET cc_start: 0.6029 (mmp) cc_final: 0.4468 (pmm) REVERT: G 96 LYS cc_start: 0.6661 (mttp) cc_final: 0.5624 (tppt) REVERT: G 122 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: G 227 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7537 (mp) REVERT: H 48 ARG cc_start: 0.7754 (ttm110) cc_final: 0.5493 (ttt-90) REVERT: H 149 ARG cc_start: 0.6969 (mtp85) cc_final: 0.6745 (mtp-110) outliers start: 20 outliers final: 16 residues processed: 173 average time/residue: 0.1097 time to fit residues: 26.1391 Evaluate side-chains 180 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 546 PHE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 784 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 227 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 94 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.0010 chunk 86 optimal weight: 0.9980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN E 27 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS G 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.179964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133110 restraints weight = 12005.606| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.91 r_work: 0.3333 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10132 Z= 0.109 Angle : 0.502 10.415 13577 Z= 0.258 Chirality : 0.037 0.192 1517 Planarity : 0.003 0.057 1591 Dihedral : 11.775 93.060 1772 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.95 % Allowed : 17.76 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.25), residues: 1149 helix: 3.16 (0.17), residues: 898 sheet: -2.09 (1.19), residues: 20 loop : -1.27 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 586 TYR 0.017 0.001 TYR G 151 PHE 0.035 0.001 PHE A 542 TRP 0.013 0.001 TRP F 178 HIS 0.007 0.001 HIS G 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10126) covalent geometry : angle 0.50159 / 0.26 (13565) SS BOND : bond 0.00161 / 0.08 ( 6) SS BOND : angle 0.79147 / 0.46 ( 12) hydrogen bonds : bond 0.03723 / 2.50 ( 741) hydrogen bonds : angle 3.37622 / 2.47 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 87 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6766 (mm-30) REVERT: E 99 PHE cc_start: 0.7115 (m-10) cc_final: 0.6836 (m-10) REVERT: E 123 MET cc_start: 0.6100 (mmp) cc_final: 0.4580 (pmm) REVERT: E 141 PHE cc_start: 0.8556 (t80) cc_final: 0.8347 (t80) REVERT: F 148 SER cc_start: 0.8865 (m) cc_final: 0.8664 (p) REVERT: G 96 LYS cc_start: 0.6604 (mttp) cc_final: 0.5647 (tppt) REVERT: G 122 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: G 227 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7425 (mp) REVERT: H 48 ARG cc_start: 0.7725 (ttm110) cc_final: 0.5320 (ttt-90) outliers start: 19 outliers final: 13 residues processed: 181 average time/residue: 0.1115 time to fit residues: 27.7684 Evaluate side-chains 178 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain G residue 20 GLN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain H residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN C 787 ASN E 27 HIS ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131722 restraints weight = 12171.911| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.71 r_work: 0.3346 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10132 Z= 0.124 Angle : 0.524 10.733 13577 Z= 0.269 Chirality : 0.038 0.180 1517 Planarity : 0.003 0.057 1591 Dihedral : 11.936 96.678 1772 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.54 % Allowed : 17.86 % Favored : 80.60 % 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: 3.32 (0.25), residues: 1149 helix: 3.08 (0.17), residues: 898 sheet: -2.01 (1.20), residues: 20 loop : -1.24 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 204 TYR 0.015 0.001 TYR G 226 PHE 0.035 0.001 PHE A 542 TRP 0.011 0.001 TRP F 178 HIS 0.007 0.001 HIS G 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10126) covalent geometry : angle 0.52381 / 0.27 (13565) SS BOND : bond 0.00174 / 0.09 ( 6) SS BOND : angle 0.87001 / 0.51 ( 12) hydrogen bonds : bond 0.03883 / 2.62 ( 741) hydrogen bonds : angle 3.45935 / 2.53 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.55 seconds wall clock time: 55 minutes 31.83 seconds (3331.83 seconds total)