Starting phenix.real_space_refine on Wed Aug 5 18:07:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6s_36013/08_2026/8j6s_36013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6s_36013/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j6s_36013/08_2026/8j6s_36013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6s_36013/08_2026/8j6s_36013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j6s_36013/08_2026/8j6s_36013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6s_36013/08_2026/8j6s_36013.map" } 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-2.2rc3-6140/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: 2.05, 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: 0.77 Conformation dependent library (CDL) restraints added in 287.7 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: 1.06 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: 1.87 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: 14880 2.52 - 5.05: 265 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: 1.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- 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 : 0.908 12.621 15181 Z= 0.706 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 0.90809 / 0.71 (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 : 0.226 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: symmetry clash REVERT: H 92 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8507 (ttp80) REVERT: E 97 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 130 ILE cc_start: 0.8796 (tp) cc_final: 0.8121 (tp) REVERT: E 131 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7983 (mtp180) REVERT: C 51 ILE cc_start: 0.8959 (mp) cc_final: 0.8345 (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: 0.8581 (tppp) REVERT: D 60 VAL cc_start: 0.9102 (t) cc_final: 0.8866 (p) REVERT: A 90 MET cc_start: 0.8099 (tmt) cc_final: 0.7262 (tmm) outliers start: 4 outliers final: 1 residues processed: 200 average time/residue: 0.1210 time to fit residues: 31.7286 Evaluate side-chains 153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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: 3.9990 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 ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.056320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.039895 restraints weight = 72807.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.041057 restraints weight = 41562.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041823 restraints weight = 29161.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.042323 restraints weight = 23178.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.042608 restraints weight = 20081.459| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10551 Z= 0.177 Angle : 0.791 10.438 15181 Z= 0.441 Chirality : 0.050 0.259 1833 Planarity : 0.006 0.080 1279 Dihedral : 31.357 173.454 3123 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 7.14 % Allowed : 33.33 % Favored : 59.52 % 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: -0.45 (0.26), residues: 897 helix: 0.28 (0.22), residues: 460 sheet: 0.59 (0.46), residues: 130 loop : -1.48 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 35 TYR 0.029 0.002 TYR H 72 PHE 0.016 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 0.00324 / 0.18 (10551) covalent geometry : angle 0.79139 / 0.44 (15181) hydrogen bonds : bond 0.06598 / 4.69 ( 651) hydrogen bonds : angle 4.77253 / 3.54 ( 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 203 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.289 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 129 ARG cc_start: 0.9677 (ttt-90) cc_final: 0.9454 (mmm160) REVERT: H 90 LEU cc_start: 0.9534 (mt) cc_final: 0.9303 (pp) REVERT: H 92 ARG cc_start: 0.9176 (mtp-110) cc_final: 0.8822 (ttp80) REVERT: H 93 GLN cc_start: 0.9474 (tp40) cc_final: 0.9034 (tm-30) REVERT: E 64 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9270 (mmmt) REVERT: E 97 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8806 (mm-30) REVERT: E 131 ARG cc_start: 0.9399 (tpp80) cc_final: 0.9005 (mtp180) REVERT: F 53 GLU cc_start: 0.9044 (tt0) cc_final: 0.8789 (tt0) REVERT: F 88 TYR cc_start: 0.8803 (m-80) cc_final: 0.8559 (m-80) REVERT: C 54 TYR cc_start: 0.9198 (m-80) cc_final: 0.8788 (m-80) REVERT: D 59 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9066 (tppp) REVERT: D 63 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8363 (mm-30) REVERT: D 67 ARG cc_start: 0.9191 (ttm170) cc_final: 0.8905 (ttm-80) REVERT: A 90 MET cc_start: 0.8361 (tmt) cc_final: 0.7911 (tmm) REVERT: A 106 ASP cc_start: 0.9338 (t70) cc_final: 0.9111 (t70) REVERT: A 120 MET cc_start: 0.8909 (mtt) cc_final: 0.8596 (mtt) outliers start: 27 outliers final: 15 residues processed: 186 average time/residue: 0.1018 time to fit residues: 26.0349 Evaluate side-chains 166 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 D residue 97 LEU 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: 0.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 83 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3511 r_free = 0.3511 target = 0.054614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038396 restraints weight = 75321.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039499 restraints weight = 43523.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040222 restraints weight = 31018.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.040613 restraints weight = 24937.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.040961 restraints weight = 21908.502| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10551 Z= 0.196 Angle : 0.771 8.373 15181 Z= 0.429 Chirality : 0.050 0.361 1833 Planarity : 0.005 0.061 1279 Dihedral : 31.499 178.753 3121 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 8.99 % Allowed : 28.57 % Favored : 62.43 % 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: -0.43 (0.26), residues: 897 helix: 0.31 (0.23), residues: 464 sheet: 0.50 (0.47), residues: 128 loop : -1.45 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 45 TYR 0.026 0.002 TYR H 72 PHE 0.022 0.003 PHE F 61 TRP 0.000 0.000 TRP L 10 HIS 0.010 0.003 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (10551) covalent geometry : angle 0.77104 / 0.43 (15181) hydrogen bonds : bond 0.07166 / 5.00 ( 651) hydrogen bonds : angle 4.46717 / 3.30 ( 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 189 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.283 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 119 ILE cc_start: 0.9465 (pt) cc_final: 0.9106 (tp) REVERT: H 44 LYS cc_start: 0.9767 (mmmt) cc_final: 0.9525 (mmmt) REVERT: H 90 LEU cc_start: 0.9550 (mt) cc_final: 0.9321 (pp) REVERT: H 92 ARG cc_start: 0.9211 (mtp-110) cc_final: 0.8842 (ttp80) REVERT: H 93 GLN cc_start: 0.9499 (tp40) cc_final: 0.9052 (tm-30) REVERT: E 97 GLU cc_start: 0.9437 (mm-30) cc_final: 0.8921 (mm-30) REVERT: E 120 MET cc_start: 0.9568 (tpp) cc_final: 0.9152 (tpp) REVERT: E 125 GLN cc_start: 0.9391 (mm-40) cc_final: 0.9014 (mm-40) REVERT: E 130 ILE cc_start: 0.9559 (tp) cc_final: 0.9127 (tp) REVERT: E 131 ARG cc_start: 0.9447 (tpp80) cc_final: 0.9191 (mtp180) REVERT: F 53 GLU cc_start: 0.9064 (tt0) cc_final: 0.8118 (tt0) REVERT: F 88 TYR cc_start: 0.8847 (m-80) cc_final: 0.8508 (m-80) REVERT: C 51 ILE cc_start: 0.8764 (mp) cc_final: 0.8523 (mp) REVERT: D 59 LYS cc_start: 0.9645 (mmmm) cc_final: 0.9302 (tppp) REVERT: D 63 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8649 (mm-30) REVERT: D 67 ARG cc_start: 0.9187 (ttm170) cc_final: 0.8935 (ttp80) REVERT: D 85 ASP cc_start: 0.8816 (m-30) cc_final: 0.8568 (t0) REVERT: A 90 MET cc_start: 0.8374 (tmt) cc_final: 0.8022 (tmm) REVERT: A 92 LEU cc_start: 0.9655 (tt) cc_final: 0.9433 (pp) REVERT: A 129 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8924 (ptm160) outliers start: 34 outliers final: 19 residues processed: 174 average time/residue: 0.0945 time to fit residues: 22.6057 Evaluate side-chains 153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 37 LEU 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 100 LEU 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 30 THR Chi-restraints excluded: chain D residue 50 ILE 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: 0.0060 chunk 28 optimal weight: 40.0000 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** 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 = 0.3465 r_free = 0.3465 target = 0.051963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.035952 restraints weight = 77757.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.037010 restraints weight = 45068.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037704 restraints weight = 32090.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038115 restraints weight = 25861.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038448 restraints weight = 22554.938| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 10551 Z= 0.300 Angle : 0.806 11.355 15181 Z= 0.453 Chirality : 0.050 0.300 1833 Planarity : 0.006 0.061 1279 Dihedral : 31.701 179.234 3121 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 10.05 % Allowed : 31.48 % Favored : 58.47 % 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: -0.39 (0.26), residues: 897 helix: 0.30 (0.22), residues: 468 sheet: 0.45 (0.46), residues: 127 loop : -1.34 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 131 TYR 0.032 0.002 TYR C 54 PHE 0.030 0.002 PHE E 67 TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.30 (10551) covalent geometry : angle 0.80551 / 0.45 (15181) hydrogen bonds : bond 0.08898 / 6.17 ( 651) hydrogen bonds : angle 4.65304 / 3.45 ( 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 180 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8521 (ttt-90) REVERT: G 104 PHE cc_start: 0.9829 (m-10) cc_final: 0.9627 (m-10) REVERT: G 119 ILE cc_start: 0.9394 (pt) cc_final: 0.9134 (tp) REVERT: H 92 ARG cc_start: 0.9209 (mtp-110) cc_final: 0.8786 (ttp80) REVERT: H 93 GLN cc_start: 0.9545 (tp40) cc_final: 0.9080 (tm-30) REVERT: E 97 GLU cc_start: 0.9497 (mm-30) cc_final: 0.8828 (mm-30) REVERT: E 125 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9054 (mm-40) REVERT: E 131 ARG cc_start: 0.9466 (tpp80) cc_final: 0.9222 (mtp180) REVERT: F 53 GLU cc_start: 0.9168 (tt0) cc_final: 0.8213 (tt0) REVERT: F 88 TYR cc_start: 0.8932 (m-80) cc_final: 0.8511 (m-80) REVERT: D 59 LYS cc_start: 0.9686 (mmmm) cc_final: 0.9323 (tppp) REVERT: D 63 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8784 (mm-30) REVERT: D 85 ASP cc_start: 0.8862 (m-30) cc_final: 0.8619 (t0) REVERT: A 90 MET cc_start: 0.8397 (tmt) cc_final: 0.8064 (tmm) REVERT: A 120 MET cc_start: 0.8699 (mtt) cc_final: 0.8227 (mtt) REVERT: A 129 ARG cc_start: 0.9202 (ttm110) cc_final: 0.8879 (ptm160) REVERT: B 44 LYS cc_start: 0.9253 (mmtm) cc_final: 0.9038 (mmtm) REVERT: B 67 ARG cc_start: 0.9686 (tpp-160) cc_final: 0.9338 (tpp-160) outliers start: 38 outliers final: 27 residues processed: 166 average time/residue: 0.0898 time to fit residues: 20.7799 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 119 ILE 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 47 SER Chi-restraints excluded: chain B residue 60 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: 40.0000 chunk 69 optimal weight: 20.0000 chunk 89 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 32 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** 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 = 0.3405 r_free = 0.3405 target = 0.048692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.032923 restraints weight = 79926.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.033895 restraints weight = 46638.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.034529 restraints weight = 33413.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.034944 restraints weight = 27016.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.035103 restraints weight = 23612.741| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3702 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= 0.355 Angle : 0.906 10.326 15181 Z= 0.496 Chirality : 0.054 0.410 1833 Planarity : 0.007 0.085 1279 Dihedral : 32.249 179.116 3121 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 31.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 10.05 % Allowed : 33.33 % Favored : 56.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.26), residues: 897 helix: -0.03 (0.22), residues: 469 sheet: 0.12 (0.48), residues: 122 loop : -1.31 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 45 TYR 0.040 0.003 TYR B 88 PHE 0.025 0.003 PHE E 67 TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.35 (10551) covalent geometry : angle 0.90565 / 0.50 (15181) hydrogen bonds : bond 0.11148 / 7.70 ( 651) hydrogen bonds : angle 4.92006 / 3.64 ( 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 177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 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 129 ARG cc_start: 0.9271 (mmm160) cc_final: 0.9004 (mmm160) REVERT: H 92 ARG cc_start: 0.9192 (mtp-110) cc_final: 0.8821 (ttp80) REVERT: H 93 GLN cc_start: 0.9571 (tp40) cc_final: 0.9083 (tm-30) REVERT: E 125 GLN cc_start: 0.9460 (mm-40) cc_final: 0.9088 (mm-40) REVERT: E 131 ARG cc_start: 0.9479 (tpp80) cc_final: 0.9155 (mtp180) REVERT: F 53 GLU cc_start: 0.9239 (tt0) cc_final: 0.8485 (tt0) REVERT: F 88 TYR cc_start: 0.8990 (m-80) cc_final: 0.8416 (m-80) REVERT: C 54 TYR cc_start: 0.9245 (m-80) cc_final: 0.8980 (m-80) REVERT: D 59 LYS cc_start: 0.9695 (mmmm) cc_final: 0.9299 (tppp) REVERT: D 63 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8724 (mm-30) REVERT: D 67 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8883 (ttm110) REVERT: D 85 ASP cc_start: 0.8869 (m-30) cc_final: 0.8600 (t0) REVERT: A 90 MET cc_start: 0.8461 (tmt) cc_final: 0.7978 (tmm) REVERT: B 55 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8991 (mtm-85) REVERT: B 67 ARG cc_start: 0.9684 (tpp-160) cc_final: 0.9213 (tpp-160) outliers start: 38 outliers final: 28 residues processed: 159 average time/residue: 0.0993 time to fit residues: 21.7242 Evaluate side-chains 153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 108 ASN Chi-restraints excluded: chain F residue 37 LEU 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 55 GLN 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 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 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3450 r_free = 0.3450 target = 0.050950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.034783 restraints weight = 78317.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035827 restraints weight = 44399.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.036509 restraints weight = 31447.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.036938 restraints weight = 25287.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.037215 restraints weight = 22097.938| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10551 Z= 0.186 Angle : 0.819 12.318 15181 Z= 0.438 Chirality : 0.051 0.374 1833 Planarity : 0.005 0.052 1279 Dihedral : 32.197 175.534 3121 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 7.94 % Allowed : 38.89 % Favored : 53.17 % 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: -0.38 (0.27), residues: 897 helix: 0.38 (0.22), residues: 469 sheet: 0.05 (0.48), residues: 124 loop : -1.24 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 92 TYR 0.017 0.002 TYR H 72 PHE 0.036 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 0.00357 / 0.19 (10551) covalent geometry : angle 0.81915 / 0.44 (15181) hydrogen bonds : bond 0.07004 / 4.84 ( 651) hydrogen bonds : angle 4.41833 / 3.25 ( 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 174 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.289 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 100 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9451 (pp) REVERT: G 104 PHE cc_start: 0.9748 (m-80) cc_final: 0.9260 (m-80) REVERT: G 120 MET cc_start: 0.9080 (pmm) cc_final: 0.8843 (pmm) REVERT: G 128 ARG cc_start: 0.9676 (mmm160) cc_final: 0.9182 (mmm160) REVERT: G 129 ARG cc_start: 0.9245 (mmm160) cc_final: 0.8917 (mmm160) REVERT: H 92 ARG cc_start: 0.9186 (mtp-110) cc_final: 0.8800 (ttp80) REVERT: H 93 GLN cc_start: 0.9560 (tp40) cc_final: 0.9084 (tm-30) REVERT: E 97 GLU cc_start: 0.9504 (mm-30) cc_final: 0.8929 (mm-30) REVERT: E 120 MET cc_start: 0.9569 (tpp) cc_final: 0.8978 (tpp) REVERT: F 88 TYR cc_start: 0.8956 (m-80) cc_final: 0.8324 (m-80) REVERT: C 54 TYR cc_start: 0.9201 (m-80) cc_final: 0.8960 (m-80) REVERT: C 94 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9123 (mm-30) REVERT: D 59 LYS cc_start: 0.9644 (mmmm) cc_final: 0.9189 (tppp) REVERT: D 63 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8700 (mm-30) REVERT: D 64 ASN cc_start: 0.9220 (m110) cc_final: 0.8715 (m-40) REVERT: D 67 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8835 (ttm110) REVERT: D 85 ASP cc_start: 0.8855 (m-30) cc_final: 0.8585 (t0) REVERT: A 90 MET cc_start: 0.8392 (tmt) cc_final: 0.7930 (tmm) REVERT: A 120 MET cc_start: 0.8997 (mtt) cc_final: 0.8760 (mtt) REVERT: B 44 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8721 (tmtt) REVERT: B 67 ARG cc_start: 0.9694 (tpp-160) cc_final: 0.9231 (tpp-160) outliers start: 30 outliers final: 21 residues processed: 161 average time/residue: 0.0940 time to fit residues: 20.8771 Evaluate side-chains 158 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 55 GLN 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 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 Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 2 optimal weight: 50.0000 chunk 104 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 7 optimal weight: 0.0370 chunk 99 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** C 108 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.051047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035013 restraints weight = 77031.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036071 restraints weight = 43746.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.036728 restraints weight = 30820.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.037176 restraints weight = 24889.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037467 restraints weight = 21653.828| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10551 Z= 0.184 Angle : 0.806 12.546 15181 Z= 0.432 Chirality : 0.050 0.358 1833 Planarity : 0.005 0.051 1279 Dihedral : 32.010 176.178 3121 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 8.20 % Allowed : 39.68 % Favored : 52.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 897 helix: 0.53 (0.23), residues: 469 sheet: 0.07 (0.48), residues: 124 loop : -1.17 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 129 TYR 0.024 0.002 TYR G 99 PHE 0.025 0.002 PHE E 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 0.00356 / 0.18 (10551) covalent geometry : angle 0.80555 / 0.43 (15181) hydrogen bonds : bond 0.06653 / 4.58 ( 651) hydrogen bonds : angle 4.26517 / 3.14 ( 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 173 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 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: G 63 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8598 (ttt-90) REVERT: G 128 ARG cc_start: 0.9674 (mmm160) cc_final: 0.9139 (mmm160) REVERT: G 129 ARG cc_start: 0.9232 (mmm160) cc_final: 0.8879 (mmm160) REVERT: H 92 ARG cc_start: 0.9184 (mtp-110) cc_final: 0.8797 (ttp80) REVERT: H 93 GLN cc_start: 0.9556 (tp40) cc_final: 0.9085 (tm-30) REVERT: E 97 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9069 (mm-30) REVERT: E 120 MET cc_start: 0.9552 (tpp) cc_final: 0.8983 (tpp) REVERT: F 88 TYR cc_start: 0.8968 (m-80) cc_final: 0.8337 (m-80) REVERT: D 59 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9172 (tppp) REVERT: D 63 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8707 (mm-30) REVERT: D 64 ASN cc_start: 0.9259 (m110) cc_final: 0.8859 (m-40) REVERT: D 67 ARG cc_start: 0.9189 (ttp80) cc_final: 0.8904 (ttm110) REVERT: D 85 ASP cc_start: 0.8884 (m-30) cc_final: 0.8595 (t0) REVERT: A 90 MET cc_start: 0.8398 (tmt) cc_final: 0.7926 (tmm) REVERT: A 97 GLU cc_start: 0.9266 (pp20) cc_final: 0.8899 (pp20) REVERT: A 120 MET cc_start: 0.8924 (mtt) cc_final: 0.8676 (mtt) REVERT: B 55 ARG cc_start: 0.9444 (OUTLIER) cc_final: 0.9018 (mmt90) REVERT: B 67 ARG cc_start: 0.9691 (tpp-160) cc_final: 0.9449 (mmp80) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.1130 time to fit residues: 24.4012 Evaluate side-chains 155 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE 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 55 GLN 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 81 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR 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 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 4 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN E 125 GLN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.052756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.036360 restraints weight = 75442.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.037456 restraints weight = 42911.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.038185 restraints weight = 30211.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.038636 restraints weight = 24108.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.038915 restraints weight = 21002.808| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10551 Z= 0.161 Angle : 0.819 15.398 15181 Z= 0.436 Chirality : 0.051 0.343 1833 Planarity : 0.005 0.075 1279 Dihedral : 31.780 175.649 3121 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 7.94 % Allowed : 41.27 % Favored : 50.79 % 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: -0.10 (0.27), residues: 897 helix: 0.57 (0.23), residues: 469 sheet: 0.13 (0.47), residues: 129 loop : -1.05 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 129 TYR 0.019 0.001 TYR B 88 PHE 0.028 0.002 PHE A 67 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 0.00309 / 0.16 (10551) covalent geometry : angle 0.81860 / 0.44 (15181) hydrogen bonds : bond 0.05657 / 3.81 ( 651) hydrogen bonds : angle 4.12466 / 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: 30 poor density : 148 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8584 (ttt-90) REVERT: G 100 LEU cc_start: 0.9734 (mm) cc_final: 0.9433 (pp) REVERT: G 128 ARG cc_start: 0.9623 (mmm160) cc_final: 0.9029 (mmm160) REVERT: G 129 ARG cc_start: 0.9197 (mmm160) cc_final: 0.8819 (mmm160) REVERT: H 92 ARG cc_start: 0.9180 (mtp-110) cc_final: 0.8821 (ttp80) REVERT: H 93 GLN cc_start: 0.9535 (tp40) cc_final: 0.9074 (tm-30) REVERT: E 97 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9036 (mm-30) REVERT: E 120 MET cc_start: 0.9497 (tpp) cc_final: 0.8681 (tpp) REVERT: E 131 ARG cc_start: 0.9461 (mtt180) cc_final: 0.9201 (mtt180) REVERT: F 53 GLU cc_start: 0.9372 (tt0) cc_final: 0.9038 (tt0) REVERT: F 88 TYR cc_start: 0.8941 (m-80) cc_final: 0.8319 (m-80) REVERT: D 59 LYS cc_start: 0.9617 (mmmm) cc_final: 0.9102 (tppp) REVERT: D 63 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8407 (mm-30) REVERT: D 64 ASN cc_start: 0.9265 (m110) cc_final: 0.8843 (m-40) REVERT: D 67 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8647 (ttm-80) REVERT: D 85 ASP cc_start: 0.8907 (m-30) cc_final: 0.8608 (t0) REVERT: A 97 GLU cc_start: 0.9213 (pp20) cc_final: 0.8834 (pp20) REVERT: A 129 ARG cc_start: 0.9247 (ttm110) cc_final: 0.8761 (ptm160) REVERT: B 40 ARG cc_start: 0.9393 (tpp80) cc_final: 0.9143 (tpp80) REVERT: B 55 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.9027 (mmt90) REVERT: B 67 ARG cc_start: 0.9669 (tpp-160) cc_final: 0.9138 (tpp-160) REVERT: B 85 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8083 (m-30) outliers start: 30 outliers final: 17 residues processed: 165 average time/residue: 0.1015 time to fit residues: 23.0938 Evaluate side-chains 156 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 55 GLN 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 81 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 50.0000 chunk 70 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** C 108 ASN ** 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 = 0.3462 r_free = 0.3462 target = 0.051429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035476 restraints weight = 76977.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.036540 restraints weight = 43661.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.037213 restraints weight = 30702.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.037675 restraints weight = 24578.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.037974 restraints weight = 21314.111| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10551 Z= 0.197 Angle : 0.826 13.192 15181 Z= 0.446 Chirality : 0.050 0.365 1833 Planarity : 0.005 0.049 1279 Dihedral : 31.738 178.392 3121 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.88 % Allowed : 42.33 % Favored : 50.79 % 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: -0.06 (0.27), residues: 897 helix: 0.60 (0.23), residues: 469 sheet: 0.18 (0.48), residues: 124 loop : -1.01 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 129 TYR 0.015 0.001 TYR H 72 PHE 0.054 0.003 PHE A 67 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 0.00395 / 0.20 (10551) covalent geometry : angle 0.82556 / 0.45 (15181) hydrogen bonds : bond 0.06503 / 4.47 ( 651) hydrogen bonds : angle 4.21539 / 3.12 ( 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 165 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8585 (ttt-90) REVERT: G 100 LEU cc_start: 0.9716 (mm) cc_final: 0.9391 (pp) REVERT: G 120 MET cc_start: 0.9086 (pmm) cc_final: 0.8694 (pmm) REVERT: G 128 ARG cc_start: 0.9637 (mmm160) cc_final: 0.9014 (mmm160) REVERT: G 129 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8813 (mmm160) REVERT: H 92 ARG cc_start: 0.9166 (mtp-110) cc_final: 0.8794 (ttp80) REVERT: H 93 GLN cc_start: 0.9550 (tp40) cc_final: 0.9065 (tm-30) REVERT: E 97 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9071 (mm-30) REVERT: F 88 TYR cc_start: 0.8961 (m-80) cc_final: 0.8355 (m-80) REVERT: D 59 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9161 (tppp) REVERT: D 63 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8760 (mm-30) REVERT: D 64 ASN cc_start: 0.9305 (m110) cc_final: 0.8839 (m110) REVERT: D 67 ARG cc_start: 0.9157 (ttp80) cc_final: 0.8827 (ttm110) REVERT: D 85 ASP cc_start: 0.8882 (m-30) cc_final: 0.8563 (t0) REVERT: A 90 MET cc_start: 0.8420 (tmt) cc_final: 0.7966 (tmm) REVERT: A 97 GLU cc_start: 0.9221 (pp20) cc_final: 0.8952 (pp20) REVERT: B 40 ARG cc_start: 0.9407 (tpp80) cc_final: 0.9143 (tpp80) REVERT: B 55 ARG cc_start: 0.9440 (OUTLIER) cc_final: 0.8900 (mmt90) REVERT: B 67 ARG cc_start: 0.9681 (tpp-160) cc_final: 0.9403 (mmp80) outliers start: 26 outliers final: 21 residues processed: 155 average time/residue: 0.1012 time to fit residues: 21.6385 Evaluate side-chains 158 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 55 GLN 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 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 B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 55 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 6.9990 chunk 92 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 35 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.051097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.035146 restraints weight = 77131.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.036198 restraints weight = 43705.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.036855 restraints weight = 30764.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037323 restraints weight = 24746.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.037624 restraints weight = 21437.865| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10551 Z= 0.201 Angle : 0.833 13.115 15181 Z= 0.448 Chirality : 0.050 0.349 1833 Planarity : 0.005 0.056 1279 Dihedral : 31.774 178.701 3121 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.08 % Allowed : 43.39 % Favored : 50.53 % 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: -0.08 (0.27), residues: 897 helix: 0.56 (0.23), residues: 468 sheet: 0.19 (0.48), residues: 124 loop : -0.97 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 129 TYR 0.015 0.001 TYR H 72 PHE 0.047 0.002 PHE A 67 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 0.00401 / 0.20 (10551) covalent geometry : angle 0.83342 / 0.45 (15181) hydrogen bonds : bond 0.06611 / 4.55 ( 651) hydrogen bonds : angle 4.27056 / 3.15 ( 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 160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8593 (ttt-90) REVERT: G 100 LEU cc_start: 0.9757 (mm) cc_final: 0.9428 (pp) REVERT: G 120 MET cc_start: 0.9058 (pmm) cc_final: 0.8670 (pmm) REVERT: G 128 ARG cc_start: 0.9634 (mmm160) cc_final: 0.9005 (mmm160) REVERT: G 129 ARG cc_start: 0.9221 (mmm160) cc_final: 0.8809 (mmm160) REVERT: H 92 ARG cc_start: 0.9159 (mtp-110) cc_final: 0.8793 (ttp80) REVERT: H 93 GLN cc_start: 0.9548 (tp40) cc_final: 0.9061 (tm-30) REVERT: E 97 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9090 (mm-30) REVERT: F 88 TYR cc_start: 0.8964 (m-80) cc_final: 0.8354 (m-80) REVERT: C 54 TYR cc_start: 0.9370 (m-80) cc_final: 0.8807 (m-80) REVERT: D 59 LYS cc_start: 0.9647 (mmmm) cc_final: 0.9159 (tppp) REVERT: D 63 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8524 (mm-30) REVERT: D 64 ASN cc_start: 0.9312 (m110) cc_final: 0.8888 (m110) REVERT: D 67 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8632 (ttm-80) REVERT: D 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8590 (t0) REVERT: A 97 GLU cc_start: 0.9231 (pp20) cc_final: 0.8965 (pp20) REVERT: A 120 MET cc_start: 0.8900 (mtt) cc_final: 0.8313 (mpp) REVERT: B 40 ARG cc_start: 0.9428 (tpp80) cc_final: 0.9163 (tpp80) REVERT: B 55 ARG cc_start: 0.9449 (OUTLIER) cc_final: 0.9048 (mmt90) REVERT: B 67 ARG cc_start: 0.9696 (tpp-160) cc_final: 0.9412 (mmp80) outliers start: 23 outliers final: 20 residues processed: 152 average time/residue: 0.0996 time to fit residues: 20.8525 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain C residue 55 GLN 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 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 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: 0.8980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 40.0000 chunk 93 optimal weight: 50.0000 chunk 77 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 overall best weight: 2.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** C 108 ASN ** 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 = 0.3463 r_free = 0.3463 target = 0.051445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035423 restraints weight = 76776.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.036481 restraints weight = 43549.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.037159 restraints weight = 30652.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.037625 restraints weight = 24574.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.037889 restraints weight = 21314.415| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10551 Z= 0.177 Angle : 0.826 14.056 15181 Z= 0.441 Chirality : 0.049 0.342 1833 Planarity : 0.004 0.049 1279 Dihedral : 31.739 178.221 3121 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.82 % Allowed : 43.92 % 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: 0.60 (0.23), residues: 468 sheet: 0.24 (0.47), residues: 129 loop : -0.96 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 129 TYR 0.015 0.001 TYR H 72 PHE 0.059 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 0.00354 / 0.18 (10551) covalent geometry : angle 0.82602 / 0.44 (15181) hydrogen bonds : bond 0.05959 / 4.07 ( 651) hydrogen bonds : angle 4.14564 / 3.07 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.67 seconds wall clock time: 33 minutes 5.08 seconds (1985.08 seconds total)