Starting phenix.real_space_refine on Fri Jul 3 00:20:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6s_36013/07_2026/8j6s_36013.cif" } resolution = 3.8 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1568 atoms to isotropic. 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 197 5.49 5 S 15 5.16 5 C 5640 2.51 5 N 1918 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10030 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 484 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 3, 'GLN:plan1': 5, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 83 Chain: "H" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 468 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 6, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 663 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 482 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2009 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 676 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 571 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 71} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 568 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 510 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 67} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2031 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain: "L" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1494 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 264} Link IDs: {'PTRANS': 9, 'TRANS': 292} Chain breaks: 7 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 962 Unresolved non-hydrogen angles: 1252 Unresolved non-hydrogen dihedrals: 822 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'GLU:plan': 11, 'TRP:plan': 8, 'HIS:plan': 10, 'ASN:plan1': 12, 'TYR:plan': 11, 'ASP:plan': 20, 'PHE:plan': 16, 'GLN:plan1': 6, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 534 Chain: "K" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 74 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 2.01, per 1000 atoms: 0.20 Number of scatterers: 10030 At special positions: 0 Unit cell: (103, 114, 113, 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 15 16.00 P 197 15.00 O 2260 8.00 N 1918 7.00 C 5640 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: 0.78 Conformation dependent library (CDL) restraints added in 184.9 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 53.2% alpha, 12.3% beta 90 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.716A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.570A pdb=" N ALA G 114 " --> pdb=" O CYS G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.800A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 3.556A pdb=" N ILE H 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 76 removed outlier: 4.098A pdb=" N ARG H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 64 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.225A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.392A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.942A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.684A pdb=" N SER C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.564A pdb=" N PHE C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.514A pdb=" N ARG D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.864A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.829A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.557A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 704 through 708 Processing sheet with id=AA1, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.940A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.016A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'L' and resid 2 through 6 removed outlier: 3.949A pdb=" N CYS L 370 " --> pdb=" O CYS L 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 21 removed outlier: 3.658A pdb=" N SER L 18 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA L 35 " --> pdb=" O SER L 18 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS L 45 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE L 58 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 74 removed outlier: 5.850A pdb=" N LYS L 94 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL L 121 " --> pdb=" O LYS L 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 132 through 137 removed outlier: 6.409A pdb=" N ALA L 153 " --> pdb=" O ILE L 166 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE L 166 " --> pdb=" O ALA L 153 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE L 155 " --> pdb=" O ILE L 164 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN L 162 " --> pdb=" O ASP L 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.438A pdb=" N LEU L 195 " --> pdb=" O ASN L 208 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN L 208 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL L 197 " --> pdb=" O ALA L 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 241 through 242 removed outlier: 4.223A pdb=" N ALA L 279 " --> pdb=" O VAL L 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 290 through 293 removed outlier: 3.751A pdb=" N SER L 342 " --> pdb=" O VAL K 684 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL K 684 " --> pdb=" O SER L 342 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 225 hydrogen bonds 434 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 149 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2473 1.34 - 1.46: 2881 1.46 - 1.58: 4782 1.58 - 1.70: 392 1.70 - 1.82: 23 Bond restraints: 10551 Sorted by residual: bond pdb=" C3' DA I 113 " pdb=" C2' DA I 113 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DG I 25 " pdb=" C2' DG I 25 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DC I 119 " pdb=" C2' DC I 119 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DG J 69 " pdb=" C2' DG J 69 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 79 " pdb=" C2' DC I 79 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 ... (remaining 10546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 14885 2.52 - 5.05: 260 5.05 - 7.57: 28 7.57 - 10.10: 6 10.10 - 12.62: 2 Bond angle restraints: 15181 Sorted by residual: angle pdb=" CA PRO C 66 " pdb=" N PRO C 66 " pdb=" CD PRO C 66 " ideal model delta sigma weight residual 112.00 103.82 8.18 1.40e+00 5.10e-01 3.42e+01 angle pdb=" CA PRO G 121 " pdb=" N PRO G 121 " pdb=" CD PRO G 121 " ideal model delta sigma weight residual 112.00 104.18 7.82 1.40e+00 5.10e-01 3.12e+01 angle pdb=" O4' DG I 55 " pdb=" C4' DG I 55 " pdb=" C3' DG I 55 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.68e+01 angle pdb=" O4' DT I 108 " pdb=" C4' DT I 108 " pdb=" C3' DT I 108 " ideal model delta sigma weight residual 106.00 103.03 2.97 6.00e-01 2.78e+00 2.45e+01 angle pdb=" O4' DG I 76 " pdb=" C4' DG I 76 " pdb=" C3' DG I 76 " ideal model delta sigma weight residual 106.00 103.11 2.89 6.00e-01 2.78e+00 2.32e+01 ... (remaining 15176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 4721 34.83 - 69.65: 1009 69.65 - 104.48: 49 104.48 - 139.31: 0 139.31 - 174.13: 4 Dihedral angle restraints: 5783 sinusoidal: 3085 harmonic: 2698 Sorted by residual: dihedral pdb=" CA MET G 120 " pdb=" C MET G 120 " pdb=" N PRO G 121 " pdb=" CA PRO G 121 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ARG G 63 " pdb=" C ARG G 63 " pdb=" N LYS G 64 " pdb=" CA LYS G 64 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1359 0.050 - 0.100: 375 0.100 - 0.149: 89 0.149 - 0.199: 7 0.199 - 0.249: 3 Chirality restraints: 1833 Sorted by residual: chirality pdb=" CA PRO C 66 " pdb=" N PRO C 66 " pdb=" C PRO C 66 " pdb=" CB PRO C 66 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO G 121 " pdb=" N PRO G 121 " pdb=" C PRO G 121 " pdb=" CB PRO G 121 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1830 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.56e+01 pdb=" N PRO G 121 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 65 " -0.074 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO C 66 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.057 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B 32 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.047 5.00e-02 4.00e+02 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 55 2.51 - 3.10: 7159 3.10 - 3.70: 18366 3.70 - 4.30: 23082 4.30 - 4.90: 33522 Nonbonded interactions: 82184 Sorted by model distance: nonbonded pdb=" NH2 ARG A 63 " pdb=" C5' DA J 33 " model vdw 1.907 3.520 nonbonded pdb=" O2 DC I 56 " pdb=" N2 DG J 92 " model vdw 2.068 2.496 nonbonded pdb=" OG1 THR H 30 " pdb=" OP1 DC I 36 " model vdw 2.098 3.040 nonbonded pdb=" O2 DC I 66 " pdb=" N2 DG J 82 " model vdw 2.104 2.496 nonbonded pdb=" OG1 THR D 80 " pdb=" OP1 DC J 75 " model vdw 2.110 3.040 ... (remaining 82179 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 59 through 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 104 or (r \ esid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 t \ hrough 124 or (resid 125 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 through 133)) selection = (chain 'C' and ((resid 59 through 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 through 63 or (resid 64 through 65 and (name N or name \ CA or name C or name O or name CB )) or resid 66 or (resid 67 through 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 124 or (r \ esid 125 and (name N or name CA or name C or name O or name CB )) or resid 126 t \ hrough 132 or (resid 133 and (name N or name CA or name C or name O or name CB ) \ ))) selection = chain 'G' } ncs_group { reference = (chain 'B' and ((resid 26 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ ame CB )) or resid 50 through 51 or (resid 52 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or resi \ d 92 through 94)) selection = (chain 'D' and ((resid 26 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 or (resid 29 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 34 or (resid 35 and (name N or na \ me CA or name C or name O or name CB )) or resid 36 through 38 or (resid 39 thro \ ugh 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thro \ ugh 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or n \ ame CB )) or resid 50 through 52 or (resid 53 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid \ 63 through 64 and (name N or name CA or name C or name O or name CB )) or resid \ 65 or (resid 66 through 85 and (name N or name CA or name C or name O or name CB \ )) or resid 86 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 through 94)) selection = (chain 'F' and (resid 26 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 38 or (resid 39 through 40 and (na \ me N or name CA or name C or name O or name CB )) or resid 41 through 52 or (res \ id 53 through 55 and (name N or name CA or name C or name O or name CB )) or res \ id 56 through 63 or (resid 64 and (name N or name CA or name C or name O or name \ CB )) or resid 65 or (resid 66 through 85 and (name N or name CA or name C or n \ ame O or name CB )) or resid 86 through 94)) selection = (chain 'H' and ((resid 26 through 30 and (name N or name CA or name C or name O \ or name CB )) or resid 31 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 48 or (resid 49 and (name N or na \ me CA or name C or name O or name CB )) or resid 50 through 71 or (resid 72 thro \ ugh 85 and (name N or name CA or name C or name O or name CB )) or resid 86 thro \ ugh 94)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.450 Find NCS groups from input model: 0.090 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 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 0.068 10551 Z= 0.474 Angle : 0.902 12.621 15181 Z= 0.700 Chirality : 0.049 0.249 1833 Planarity : 0.007 0.126 1279 Dihedral : 29.579 174.135 4015 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.06 % Allowed : 38.36 % Favored : 60.58 % 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: -0.40 (0.27), residues: 897 helix: 0.23 (0.23), residues: 457 sheet: 1.13 (0.47), residues: 126 loop : -1.51 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 36 TYR 0.044 0.002 TYR H 72 PHE 0.022 0.002 PHE E 84 TRP 0.000 0.000 TRP L 10 HIS 0.013 0.004 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.47 (10551) covalent geometry : angle 0.90234 / 0.70 (15181) hydrogen bonds : bond 0.16855 / 11.99 ( 651) hydrogen bonds : angle 6.28185 / 4.74 ( 1667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8508 (ttp80) REVERT: E 97 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8020 (mm-30) REVERT: E 130 ILE cc_start: 0.8796 (tp) cc_final: 0.8119 (tp) REVERT: E 131 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7980 (mtp180) REVERT: C 51 ILE cc_start: 0.8959 (mp) cc_final: 0.8346 (mp) REVERT: C 93 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 59 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8582 (tppp) REVERT: D 60 VAL cc_start: 0.9102 (t) cc_final: 0.8865 (p) REVERT: A 90 MET cc_start: 0.8099 (tmt) cc_final: 0.7265 (tmm) outliers start: 4 outliers final: 1 residues processed: 200 average time/residue: 0.1062 time to fit residues: 27.9604 Evaluate side-chains 151 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 0.0050 chunk 38 optimal weight: 20.0000 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 108 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN D 64 ASN D 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.056236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.040055 restraints weight = 71859.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.041212 restraints weight = 41109.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.041966 restraints weight = 28885.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.042399 restraints weight = 23002.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042567 restraints weight = 20075.708| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10551 Z= 0.181 Angle : 0.787 10.654 15181 Z= 0.440 Chirality : 0.050 0.289 1833 Planarity : 0.006 0.077 1279 Dihedral : 31.445 172.930 3123 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 7.41 % Allowed : 33.33 % Favored : 59.26 % 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: -0.42 (0.26), residues: 897 helix: 0.29 (0.22), residues: 457 sheet: 0.55 (0.46), residues: 130 loop : -1.40 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 45 TYR 0.030 0.002 TYR H 72 PHE 0.017 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.007 0.003 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (10551) covalent geometry : angle 0.78713 / 0.44 (15181) hydrogen bonds : bond 0.06496 / 4.55 ( 651) hydrogen bonds : angle 4.69458 / 3.48 ( 1667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 90 LEU cc_start: 0.9532 (mt) cc_final: 0.9302 (pp) REVERT: H 92 ARG cc_start: 0.9177 (mtp-110) cc_final: 0.8817 (ttp80) REVERT: H 93 GLN cc_start: 0.9468 (tp40) cc_final: 0.9035 (tm-30) REVERT: E 64 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9267 (mmmt) REVERT: E 130 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9207 (tp) REVERT: E 131 ARG cc_start: 0.9408 (tpp80) cc_final: 0.8933 (mtp180) REVERT: F 53 GLU cc_start: 0.9078 (tt0) cc_final: 0.8876 (tt0) REVERT: F 88 TYR cc_start: 0.8835 (m-80) cc_final: 0.8578 (m-80) REVERT: C 54 TYR cc_start: 0.9221 (m-80) cc_final: 0.8873 (m-80) REVERT: D 59 LYS cc_start: 0.9626 (mmmm) cc_final: 0.9066 (tppp) REVERT: D 63 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8395 (mm-30) REVERT: D 67 ARG cc_start: 0.9198 (ttm170) cc_final: 0.8908 (ttm-80) REVERT: A 90 MET cc_start: 0.8368 (tmt) cc_final: 0.7924 (tmm) REVERT: A 106 ASP cc_start: 0.9318 (t70) cc_final: 0.9053 (t70) outliers start: 28 outliers final: 14 residues processed: 185 average time/residue: 0.0838 time to fit residues: 21.7604 Evaluate side-chains 167 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 chunk 52 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 88 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 108 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.053600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.037559 restraints weight = 75643.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.038632 restraints weight = 43531.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039369 restraints weight = 30981.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.039630 restraints weight = 24862.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.040045 restraints weight = 22377.832| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10551 Z= 0.237 Angle : 0.776 8.152 15181 Z= 0.437 Chirality : 0.050 0.453 1833 Planarity : 0.006 0.059 1279 Dihedral : 31.670 179.343 3121 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 8.20 % Allowed : 33.86 % Favored : 57.94 % 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: -0.36 (0.27), residues: 897 helix: 0.35 (0.23), residues: 465 sheet: 0.56 (0.46), residues: 126 loop : -1.40 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 45 TYR 0.026 0.002 TYR H 72 PHE 0.016 0.002 PHE B 61 TRP 0.000 0.000 TRP L 10 HIS 0.007 0.003 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.24 (10551) covalent geometry : angle 0.77614 / 0.44 (15181) hydrogen bonds : bond 0.08271 / 5.77 ( 651) hydrogen bonds : angle 4.49152 / 3.34 ( 1667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.8739 (pmm) cc_final: 0.8509 (pmm) REVERT: H 90 LEU cc_start: 0.9560 (mt) cc_final: 0.9337 (pp) REVERT: H 92 ARG cc_start: 0.9215 (mtp-110) cc_final: 0.8847 (ttp80) REVERT: H 93 GLN cc_start: 0.9512 (tp40) cc_final: 0.9058 (tm-30) REVERT: E 97 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8916 (mm-30) REVERT: E 120 MET cc_start: 0.9578 (tpp) cc_final: 0.9140 (tpp) REVERT: E 125 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9056 (mm-40) REVERT: E 131 ARG cc_start: 0.9417 (tpp80) cc_final: 0.9149 (mtp180) REVERT: F 53 GLU cc_start: 0.9082 (tt0) cc_final: 0.8217 (tt0) REVERT: F 88 TYR cc_start: 0.8867 (m-80) cc_final: 0.8520 (m-80) REVERT: D 59 LYS cc_start: 0.9636 (mmmm) cc_final: 0.9249 (tppp) REVERT: D 63 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8627 (mm-30) REVERT: D 67 ARG cc_start: 0.9205 (ttm170) cc_final: 0.9004 (ttp80) REVERT: D 85 ASP cc_start: 0.8835 (m-30) cc_final: 0.8591 (t0) REVERT: A 90 MET cc_start: 0.8380 (tmt) cc_final: 0.8057 (tmm) REVERT: A 92 LEU cc_start: 0.9663 (tt) cc_final: 0.9455 (pp) REVERT: A 129 ARG cc_start: 0.9148 (ttm110) cc_final: 0.8919 (ptm160) outliers start: 31 outliers final: 19 residues processed: 169 average time/residue: 0.0889 time to fit residues: 20.6855 Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 14 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 105 optimal weight: 50.0000 chunk 73 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.052326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.036440 restraints weight = 75771.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037496 restraints weight = 44118.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038153 restraints weight = 31575.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.038657 restraints weight = 25527.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.038821 restraints weight = 22030.783| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10551 Z= 0.253 Angle : 0.759 8.780 15181 Z= 0.429 Chirality : 0.049 0.312 1833 Planarity : 0.005 0.051 1279 Dihedral : 31.809 178.106 3121 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 9.26 % Allowed : 32.54 % Favored : 58.20 % 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: -0.27 (0.26), residues: 897 helix: 0.45 (0.23), residues: 468 sheet: 0.41 (0.46), residues: 127 loop : -1.33 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 131 TYR 0.021 0.002 TYR H 72 PHE 0.016 0.002 PHE G 104 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.25 (10551) covalent geometry : angle 0.75950 / 0.43 (15181) hydrogen bonds : bond 0.07916 / 5.48 ( 651) hydrogen bonds : angle 4.52466 / 3.36 ( 1667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8639 (ttt90) REVERT: G 119 ILE cc_start: 0.9408 (pt) cc_final: 0.9111 (tp) REVERT: H 92 ARG cc_start: 0.9215 (mtp-110) cc_final: 0.8822 (ttp80) REVERT: H 93 GLN cc_start: 0.9539 (tp40) cc_final: 0.9081 (tm-30) REVERT: E 97 GLU cc_start: 0.9520 (mm-30) cc_final: 0.8837 (mm-30) REVERT: E 131 ARG cc_start: 0.9409 (tpp80) cc_final: 0.9150 (mtp180) REVERT: F 88 TYR cc_start: 0.8938 (m-80) cc_final: 0.8525 (m-80) REVERT: D 59 LYS cc_start: 0.9654 (mmmm) cc_final: 0.9255 (tppp) REVERT: D 63 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 85 ASP cc_start: 0.8840 (m-30) cc_final: 0.8580 (t0) REVERT: A 90 MET cc_start: 0.8408 (tmt) cc_final: 0.8090 (tmm) REVERT: A 120 MET cc_start: 0.8678 (mtt) cc_final: 0.8200 (mtt) REVERT: A 129 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8876 (ptm160) REVERT: B 67 ARG cc_start: 0.9694 (tpp-160) cc_final: 0.9335 (tpp-160) outliers start: 35 outliers final: 26 residues processed: 167 average time/residue: 0.0929 time to fit residues: 21.4048 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 89 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 overall best weight: 8.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.048480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.032756 restraints weight = 82374.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.033711 restraints weight = 47757.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034345 restraints weight = 34287.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034744 restraints weight = 27823.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034898 restraints weight = 24317.379| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 10551 Z= 0.384 Angle : 0.915 10.379 15181 Z= 0.504 Chirality : 0.054 0.306 1833 Planarity : 0.007 0.083 1279 Dihedral : 32.329 179.440 3121 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 34.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 10.85 % Allowed : 33.33 % Favored : 55.82 % 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: -0.85 (0.26), residues: 897 helix: -0.16 (0.21), residues: 469 sheet: 0.04 (0.47), residues: 122 loop : -1.26 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 92 TYR 0.055 0.003 TYR B 88 PHE 0.034 0.004 PHE C 84 TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00714 / 0.38 (10551) covalent geometry : angle 0.91466 / 0.50 (15181) hydrogen bonds : bond 0.12823 / 8.85 ( 651) hydrogen bonds : angle 5.07828 / 3.78 ( 1667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8633 (ttt90) REVERT: G 104 PHE cc_start: 0.9818 (m-80) cc_final: 0.9459 (m-80) REVERT: G 119 ILE cc_start: 0.9445 (pt) cc_final: 0.9143 (tp) REVERT: G 120 MET cc_start: 0.8998 (pmm) cc_final: 0.8693 (pmm) REVERT: G 129 ARG cc_start: 0.9196 (mmm160) cc_final: 0.8985 (mmm160) REVERT: H 92 ARG cc_start: 0.9195 (mtp-110) cc_final: 0.8785 (ttp80) REVERT: H 93 GLN cc_start: 0.9576 (tp40) cc_final: 0.9078 (tm-30) REVERT: E 97 GLU cc_start: 0.9577 (mm-30) cc_final: 0.8727 (mm-30) REVERT: E 125 GLN cc_start: 0.9538 (mm-40) cc_final: 0.9085 (mm-40) REVERT: F 31 LYS cc_start: 0.9750 (OUTLIER) cc_final: 0.9261 (ttmm) REVERT: F 88 TYR cc_start: 0.8979 (m-80) cc_final: 0.8432 (m-80) REVERT: D 59 LYS cc_start: 0.9694 (mmmm) cc_final: 0.9312 (tppp) REVERT: D 63 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8851 (mm-30) REVERT: D 85 ASP cc_start: 0.8828 (m-30) cc_final: 0.8566 (t0) REVERT: A 90 MET cc_start: 0.8409 (tmt) cc_final: 0.7944 (tmm) REVERT: B 55 ARG cc_start: 0.9482 (OUTLIER) cc_final: 0.8996 (mtm-85) REVERT: B 67 ARG cc_start: 0.9699 (tpp-160) cc_final: 0.9257 (tpp-160) outliers start: 41 outliers final: 30 residues processed: 158 average time/residue: 0.0902 time to fit residues: 19.8066 Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.035362 restraints weight = 77498.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036436 restraints weight = 43789.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.037137 restraints weight = 30844.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037582 restraints weight = 24664.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.037859 restraints weight = 21428.409| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10551 Z= 0.175 Angle : 0.801 12.426 15181 Z= 0.431 Chirality : 0.051 0.399 1833 Planarity : 0.005 0.067 1279 Dihedral : 32.273 174.547 3121 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 8.73 % Allowed : 38.36 % Favored : 52.91 % 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: -0.29 (0.27), residues: 897 helix: 0.48 (0.23), residues: 470 sheet: 0.04 (0.48), residues: 124 loop : -1.24 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 116 TYR 0.019 0.002 TYR C 54 PHE 0.021 0.002 PHE C 104 TRP 0.000 0.000 TRP L 10 HIS 0.007 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (10551) covalent geometry : angle 0.80099 / 0.43 (15181) hydrogen bonds : bond 0.06549 / 4.51 ( 651) hydrogen bonds : angle 4.33799 / 3.20 ( 1667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 PHE cc_start: 0.9804 (m-80) cc_final: 0.9589 (m-10) REVERT: G 119 ILE cc_start: 0.9344 (pt) cc_final: 0.9054 (tp) REVERT: G 128 ARG cc_start: 0.9654 (mmm160) cc_final: 0.9173 (mmm160) REVERT: G 129 ARG cc_start: 0.9204 (mmm160) cc_final: 0.8919 (mmm160) REVERT: H 92 ARG cc_start: 0.9184 (mtp-110) cc_final: 0.8812 (ttp80) REVERT: H 93 GLN cc_start: 0.9538 (tp40) cc_final: 0.9077 (tm-30) REVERT: E 97 GLU cc_start: 0.9511 (mm-30) cc_final: 0.8848 (mm-30) REVERT: F 88 TYR cc_start: 0.8961 (m-80) cc_final: 0.8330 (m-80) REVERT: C 90 MET cc_start: 0.9020 (tpp) cc_final: 0.8618 (tpp) REVERT: D 59 LYS cc_start: 0.9623 (mmmm) cc_final: 0.9229 (tppp) REVERT: D 63 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8346 (mm-30) REVERT: D 67 ARG cc_start: 0.9154 (ttp80) cc_final: 0.8556 (ttm-80) REVERT: D 85 ASP cc_start: 0.8807 (m-30) cc_final: 0.8536 (t0) REVERT: A 90 MET cc_start: 0.8445 (tmt) cc_final: 0.8000 (tmm) REVERT: A 120 MET cc_start: 0.8932 (mtt) cc_final: 0.8369 (mtt) REVERT: A 129 ARG cc_start: 0.9234 (ttm110) cc_final: 0.8771 (ptm160) REVERT: B 67 ARG cc_start: 0.9695 (tpp-160) cc_final: 0.9213 (tpp-160) outliers start: 33 outliers final: 25 residues processed: 162 average time/residue: 0.0906 time to fit residues: 20.2341 Evaluate side-chains 160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.050724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034765 restraints weight = 76864.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035799 restraints weight = 43912.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036497 restraints weight = 31103.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.036939 restraints weight = 24908.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037217 restraints weight = 21634.071| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10551 Z= 0.210 Angle : 0.811 15.120 15181 Z= 0.436 Chirality : 0.050 0.307 1833 Planarity : 0.005 0.050 1279 Dihedral : 32.144 176.283 3121 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 8.20 % Allowed : 40.74 % Favored : 51.06 % 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: -0.26 (0.27), residues: 897 helix: 0.49 (0.23), residues: 469 sheet: 0.06 (0.48), residues: 124 loop : -1.18 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 45 TYR 0.017 0.002 TYR C 54 PHE 0.045 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.21 (10551) covalent geometry : angle 0.81095 / 0.44 (15181) hydrogen bonds : bond 0.07287 / 5.03 ( 651) hydrogen bonds : angle 4.37385 / 3.23 ( 1667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 PHE cc_start: 0.9798 (m-80) cc_final: 0.9588 (m-10) REVERT: G 128 ARG cc_start: 0.9648 (mmm160) cc_final: 0.9138 (mmm160) REVERT: G 129 ARG cc_start: 0.9196 (mmm160) cc_final: 0.8913 (mmm160) REVERT: H 92 ARG cc_start: 0.9186 (mtp-110) cc_final: 0.8796 (ttp80) REVERT: H 93 GLN cc_start: 0.9560 (tp40) cc_final: 0.9083 (tm-30) REVERT: E 97 GLU cc_start: 0.9532 (mm-30) cc_final: 0.8888 (mm-30) REVERT: E 120 MET cc_start: 0.9401 (mmm) cc_final: 0.8299 (mtt) REVERT: F 88 TYR cc_start: 0.8986 (m-80) cc_final: 0.8373 (m-80) REVERT: C 90 MET cc_start: 0.9051 (tpp) cc_final: 0.8715 (tpp) REVERT: D 59 LYS cc_start: 0.9631 (mmmm) cc_final: 0.9184 (tppp) REVERT: D 63 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8742 (mm-30) REVERT: D 67 ARG cc_start: 0.9149 (ttp80) cc_final: 0.8865 (ttm110) REVERT: D 85 ASP cc_start: 0.8868 (m-30) cc_final: 0.8582 (t0) REVERT: A 90 MET cc_start: 0.8391 (tmt) cc_final: 0.7934 (tmm) REVERT: A 97 GLU cc_start: 0.9275 (pp20) cc_final: 0.8910 (pp20) REVERT: A 120 MET cc_start: 0.8875 (mtt) cc_final: 0.8675 (mtt) REVERT: B 55 ARG cc_start: 0.9456 (OUTLIER) cc_final: 0.9035 (mmt90) REVERT: B 67 ARG cc_start: 0.9694 (tpp-160) cc_final: 0.9211 (tpp-160) outliers start: 31 outliers final: 24 residues processed: 158 average time/residue: 0.0885 time to fit residues: 19.0741 Evaluate side-chains 158 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 3.9990 chunk 95 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.052106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.036242 restraints weight = 74064.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037313 restraints weight = 42164.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038020 restraints weight = 29662.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.038296 restraints weight = 23567.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038727 restraints weight = 21096.048| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10551 Z= 0.158 Angle : 0.805 14.691 15181 Z= 0.427 Chirality : 0.050 0.353 1833 Planarity : 0.005 0.053 1279 Dihedral : 31.975 175.284 3121 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 8.47 % Allowed : 40.48 % Favored : 51.06 % 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: -0.05 (0.27), residues: 897 helix: 0.66 (0.23), residues: 469 sheet: 0.12 (0.47), residues: 129 loop : -1.10 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 129 TYR 0.017 0.001 TYR H 72 PHE 0.022 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.007 0.003 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (10551) covalent geometry : angle 0.80478 / 0.43 (15181) hydrogen bonds : bond 0.05748 / 3.91 ( 651) hydrogen bonds : angle 4.11052 / 3.04 ( 1667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.9162 (pmm) cc_final: 0.8913 (pmm) REVERT: G 128 ARG cc_start: 0.9625 (mmm160) cc_final: 0.9063 (mmm160) REVERT: G 129 ARG cc_start: 0.9221 (mmm160) cc_final: 0.8900 (mmm160) REVERT: H 92 ARG cc_start: 0.9162 (mtp-110) cc_final: 0.8794 (ttp80) REVERT: H 93 GLN cc_start: 0.9536 (tp40) cc_final: 0.9065 (tm-30) REVERT: E 97 GLU cc_start: 0.9534 (mm-30) cc_final: 0.8919 (mm-30) REVERT: E 125 GLN cc_start: 0.9541 (mm-40) cc_final: 0.9121 (mm110) REVERT: F 53 GLU cc_start: 0.9268 (tt0) cc_final: 0.8196 (tt0) REVERT: F 88 TYR cc_start: 0.8968 (m-80) cc_final: 0.8327 (m-80) REVERT: C 54 TYR cc_start: 0.9216 (m-80) cc_final: 0.8985 (m-80) REVERT: C 90 MET cc_start: 0.9120 (tpp) cc_final: 0.8702 (tpp) REVERT: D 59 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9153 (tppp) REVERT: D 63 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8696 (mm-30) REVERT: D 67 ARG cc_start: 0.9131 (ttp80) cc_final: 0.8837 (ttm110) REVERT: D 85 ASP cc_start: 0.8938 (m-30) cc_final: 0.8631 (t0) REVERT: A 90 MET cc_start: 0.8400 (tmt) cc_final: 0.7969 (tmm) REVERT: A 97 GLU cc_start: 0.9237 (pp20) cc_final: 0.8854 (pp20) REVERT: B 55 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.8982 (mmt90) REVERT: B 67 ARG cc_start: 0.9689 (tpp-160) cc_final: 0.9445 (mmp80) outliers start: 32 outliers final: 26 residues processed: 166 average time/residue: 0.0837 time to fit residues: 19.0990 Evaluate side-chains 164 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 94 optimal weight: 0.0270 chunk 34 optimal weight: 20.0000 overall best weight: 1.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.051998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036017 restraints weight = 75959.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037087 restraints weight = 42945.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037771 restraints weight = 30122.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.038235 restraints weight = 24153.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038395 restraints weight = 20913.167| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10551 Z= 0.170 Angle : 0.819 14.713 15181 Z= 0.434 Chirality : 0.049 0.356 1833 Planarity : 0.004 0.047 1279 Dihedral : 31.871 176.985 3121 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.94 % Allowed : 41.80 % Favored : 50.26 % 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: 0.02 (0.27), residues: 897 helix: 0.69 (0.23), residues: 469 sheet: 0.21 (0.47), residues: 129 loop : -1.06 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 129 TYR 0.016 0.001 TYR H 72 PHE 0.057 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (10551) covalent geometry : angle 0.81867 / 0.43 (15181) hydrogen bonds : bond 0.05966 / 4.08 ( 651) hydrogen bonds : angle 4.09838 / 3.03 ( 1667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.9031 (pmm) cc_final: 0.8775 (pmm) REVERT: G 128 ARG cc_start: 0.9620 (mmm160) cc_final: 0.9052 (mmm160) REVERT: G 129 ARG cc_start: 0.9219 (mmm160) cc_final: 0.8903 (mmm160) REVERT: H 92 ARG cc_start: 0.9172 (mtp-110) cc_final: 0.8802 (ttp80) REVERT: H 93 GLN cc_start: 0.9541 (tp40) cc_final: 0.9072 (tm-30) REVERT: E 97 GLU cc_start: 0.9545 (mm-30) cc_final: 0.8985 (mm-30) REVERT: E 120 MET cc_start: 0.9125 (mmm) cc_final: 0.8193 (mtt) REVERT: F 88 TYR cc_start: 0.8958 (m-80) cc_final: 0.8295 (m-80) REVERT: C 54 TYR cc_start: 0.9232 (m-80) cc_final: 0.9006 (m-80) REVERT: C 90 MET cc_start: 0.9117 (tpp) cc_final: 0.8698 (tpp) REVERT: D 59 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9147 (tppp) REVERT: D 63 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8473 (mm-30) REVERT: D 67 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8592 (ttm-80) REVERT: D 85 ASP cc_start: 0.8869 (m-30) cc_final: 0.8578 (t0) REVERT: A 90 MET cc_start: 0.8365 (tmt) cc_final: 0.7923 (tmm) REVERT: A 97 GLU cc_start: 0.9215 (pp20) cc_final: 0.8844 (pp20) REVERT: A 129 ARG cc_start: 0.9263 (ttm110) cc_final: 0.8861 (ptm160) REVERT: B 55 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.9065 (mmt90) REVERT: B 67 ARG cc_start: 0.9690 (tpp-160) cc_final: 0.9440 (mmp80) outliers start: 30 outliers final: 24 residues processed: 161 average time/residue: 0.0945 time to fit residues: 20.8191 Evaluate side-chains 163 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 0.0870 chunk 92 optimal weight: 40.0000 chunk 106 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 70 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 125 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.052066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036158 restraints weight = 75350.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.037250 restraints weight = 42610.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.037952 restraints weight = 29837.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038414 restraints weight = 23795.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.038691 restraints weight = 20602.615| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10551 Z= 0.169 Angle : 0.820 14.352 15181 Z= 0.435 Chirality : 0.049 0.375 1833 Planarity : 0.004 0.048 1279 Dihedral : 31.825 177.643 3121 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.61 % Allowed : 43.92 % Favored : 49.47 % 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: 0.09 (0.27), residues: 897 helix: 0.78 (0.23), residues: 468 sheet: 0.24 (0.47), residues: 129 loop : -1.07 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 116 TYR 0.016 0.001 TYR H 72 PHE 0.058 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (10551) covalent geometry : angle 0.81992 / 0.43 (15181) hydrogen bonds : bond 0.05863 / 4.00 ( 651) hydrogen bonds : angle 4.04764 / 3.00 ( 1667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 120 MET cc_start: 0.9037 (pmm) cc_final: 0.8741 (pmm) REVERT: G 128 ARG cc_start: 0.9620 (mmm160) cc_final: 0.9054 (mmm160) REVERT: G 129 ARG cc_start: 0.9228 (mmm160) cc_final: 0.8893 (mmm160) REVERT: H 92 ARG cc_start: 0.9155 (mtp-110) cc_final: 0.8798 (ttp80) REVERT: H 93 GLN cc_start: 0.9528 (tp40) cc_final: 0.9061 (tm-30) REVERT: E 97 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9003 (mm-30) REVERT: E 120 MET cc_start: 0.9103 (mmm) cc_final: 0.7677 (mtt) REVERT: F 39 ARG cc_start: 0.9633 (OUTLIER) cc_final: 0.9253 (tpp80) REVERT: F 88 TYR cc_start: 0.8958 (m-80) cc_final: 0.8332 (m-80) REVERT: C 54 TYR cc_start: 0.9220 (m-80) cc_final: 0.9004 (m-80) REVERT: C 90 MET cc_start: 0.9152 (tpp) cc_final: 0.8723 (tpp) REVERT: D 59 LYS cc_start: 0.9616 (mmmm) cc_final: 0.9116 (tppp) REVERT: D 63 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8505 (mm-30) REVERT: D 67 ARG cc_start: 0.9123 (ttp80) cc_final: 0.8608 (ttm-80) REVERT: D 85 ASP cc_start: 0.8898 (m-30) cc_final: 0.8596 (t0) REVERT: A 97 GLU cc_start: 0.9231 (pp20) cc_final: 0.8847 (pp20) REVERT: A 129 ARG cc_start: 0.9268 (ttm110) cc_final: 0.8855 (ptm160) REVERT: B 55 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.9068 (mmt90) REVERT: B 67 ARG cc_start: 0.9691 (tpp-160) cc_final: 0.9440 (mmp80) outliers start: 25 outliers final: 22 residues processed: 159 average time/residue: 0.0967 time to fit residues: 21.1117 Evaluate side-chains 162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 50.0000 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 75 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 77 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 92 optimal weight: 50.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.052328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036389 restraints weight = 74963.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.037476 restraints weight = 42439.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038169 restraints weight = 29742.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.038592 restraints weight = 23788.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.038934 restraints weight = 20623.649| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10551 Z= 0.162 Angle : 0.818 14.918 15181 Z= 0.433 Chirality : 0.049 0.376 1833 Planarity : 0.004 0.048 1279 Dihedral : 31.788 177.832 3121 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.35 % Allowed : 44.44 % Favored : 49.21 % 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: 0.13 (0.27), residues: 897 helix: 0.80 (0.23), residues: 467 sheet: 0.27 (0.47), residues: 129 loop : -1.02 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 129 TYR 0.016 0.001 TYR H 72 PHE 0.056 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (10551) covalent geometry : angle 0.81818 / 0.43 (15181) hydrogen bonds : bond 0.05683 / 3.87 ( 651) hydrogen bonds : angle 3.97648 / 2.96 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.14 seconds wall clock time: 30 minutes 18.02 seconds (1818.02 seconds total)