Starting phenix.real_space_refine on Wed Sep 17 20:23:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6s_36013/09_2025/8j6s_36013.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1568 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 197 5.49 5 S 15 5.16 5 C 5640 2.51 5 N 1918 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 2.62, per 1000 atoms: 0.26 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: 1.05 Conformation dependent library (CDL) restraints added in 350.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.60 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: 2.18 Time building geometry restraints manager: 1.38 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=" CB MET E 120 " pdb=" CG MET E 120 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.492 1.560 -0.068 5.00e-02 4.00e+02 1.87e+00 bond pdb=" C3' DC J 75 " pdb=" O3' DC J 75 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN E 68 " pdb=" CG GLN E 68 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB PRO C 66 " pdb=" CG PRO C 66 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.49e+00 ... (remaining 10546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 14969 2.52 - 5.05: 176 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=" CA ARG B 36 " pdb=" CB ARG B 36 " pdb=" CG ARG B 36 " ideal model delta sigma weight residual 114.10 123.36 -9.26 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CB MET E 120 " pdb=" CG MET E 120 " pdb=" SD MET E 120 " ideal model delta sigma weight residual 112.70 125.32 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" CA ARG B 92 " pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+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: 1486 0.050 - 0.099: 270 0.099 - 0.149: 67 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.700 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.004 0.068 10551 Z= 0.189 Angle : 0.795 12.621 15181 Z= 0.456 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00416 (10551) covalent geometry : angle 0.79481 (15181) hydrogen bonds : bond 0.16855 ( 651) hydrogen bonds : angle 6.28185 ( 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 : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 92 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8508 (ttp80) REVERT: E 97 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8020 (mm-30) REVERT: E 130 ILE cc_start: 0.8796 (tp) cc_final: 0.8119 (tp) REVERT: E 131 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7980 (mtp180) REVERT: C 51 ILE cc_start: 0.8959 (mp) cc_final: 0.8346 (mp) REVERT: C 93 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7623 (tm-30) REVERT: D 59 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8582 (tppp) REVERT: D 60 VAL cc_start: 0.9102 (t) cc_final: 0.8865 (p) REVERT: A 90 MET cc_start: 0.8099 (tmt) cc_final: 0.7265 (tmm) outliers start: 4 outliers final: 1 residues processed: 200 average time/residue: 0.1478 time to fit residues: 38.1778 Evaluate side-chains 151 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 0.0050 chunk 38 optimal weight: 7.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3546 r_free = 0.3546 target = 0.056241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.040199 restraints weight = 71660.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041374 restraints weight = 40541.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042148 restraints weight = 28247.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.042670 restraints weight = 22312.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.042849 restraints weight = 19160.899| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10551 Z= 0.168 Angle : 0.711 9.764 15181 Z= 0.397 Chirality : 0.041 0.242 1833 Planarity : 0.005 0.068 1279 Dihedral : 31.291 179.938 3123 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.61 % Allowed : 32.01 % Favored : 61.38 % 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 aren not related in a simple way. whole: -0.05 (0.27), residues: 897 helix: 0.55 (0.22), residues: 468 sheet: 0.95 (0.47), residues: 129 loop : -1.33 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 45 TYR 0.030 0.002 TYR H 72 PHE 0.015 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.008 0.003 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00364 (10551) covalent geometry : angle 0.71066 (15181) hydrogen bonds : bond 0.05480 ( 651) hydrogen bonds : angle 4.22695 ( 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 192 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.282 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 128 ARG cc_start: 0.9524 (tpp80) cc_final: 0.9263 (mmm160) REVERT: G 129 ARG cc_start: 0.9689 (ttt-90) cc_final: 0.9361 (mmm160) REVERT: H 90 LEU cc_start: 0.9554 (mt) cc_final: 0.9328 (pp) REVERT: H 92 ARG cc_start: 0.9202 (mtp-110) cc_final: 0.8820 (ttp80) REVERT: H 93 GLN cc_start: 0.9480 (tp40) cc_final: 0.9030 (tm-30) REVERT: E 109 LEU cc_start: 0.9424 (mt) cc_final: 0.9185 (mt) REVERT: F 88 TYR cc_start: 0.8859 (m-80) cc_final: 0.8538 (m-80) REVERT: C 50 GLU cc_start: 0.9041 (tt0) cc_final: 0.8724 (mp0) REVERT: D 59 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9102 (mmmm) REVERT: D 63 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8709 (mm-30) REVERT: D 67 ARG cc_start: 0.9190 (ttm170) cc_final: 0.8967 (ttp80) REVERT: A 90 MET cc_start: 0.8439 (tmt) cc_final: 0.7597 (tmm) REVERT: A 94 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8401 (mm-30) REVERT: A 106 ASP cc_start: 0.9316 (t70) cc_final: 0.8996 (t70) REVERT: A 129 ARG cc_start: 0.9225 (ttp-170) cc_final: 0.8996 (ttm110) outliers start: 25 outliers final: 10 residues processed: 183 average time/residue: 0.1187 time to fit residues: 29.5062 Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 113 HIS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN C 68 GLN C 85 GLN C 108 ASN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.054980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039078 restraints weight = 72681.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040193 restraints weight = 41749.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.040956 restraints weight = 29451.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.041440 restraints weight = 23397.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.041613 restraints weight = 20203.438| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10551 Z= 0.182 Angle : 0.687 12.961 15181 Z= 0.381 Chirality : 0.041 0.330 1833 Planarity : 0.005 0.051 1279 Dihedral : 31.281 179.065 3121 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.56 % Allowed : 34.66 % Favored : 59.79 % 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 aren not related in a simple way. whole: 0.17 (0.27), residues: 897 helix: 0.78 (0.23), residues: 468 sheet: 0.93 (0.48), residues: 129 loop : -1.26 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 45 TYR 0.025 0.002 TYR H 72 PHE 0.017 0.001 PHE C 84 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00402 (10551) covalent geometry : angle 0.68658 (15181) hydrogen bonds : bond 0.05638 ( 651) hydrogen bonds : angle 3.94661 ( 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 174 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.351 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: 0.9192 (OUTLIER) cc_final: 0.8708 (ttt90) REVERT: G 119 ILE cc_start: 0.9228 (pt) cc_final: 0.8972 (mp) REVERT: G 128 ARG cc_start: 0.9520 (tpp80) cc_final: 0.8663 (mmm160) REVERT: G 129 ARG cc_start: 0.9702 (ttt-90) cc_final: 0.9370 (mmm160) REVERT: H 92 ARG cc_start: 0.9213 (mtp-110) cc_final: 0.8811 (ttp80) REVERT: E 90 MET cc_start: 0.9193 (mmm) cc_final: 0.8970 (mmm) REVERT: E 125 GLN cc_start: 0.9527 (mm-40) cc_final: 0.9133 (mm-40) REVERT: F 39 ARG cc_start: 0.9640 (OUTLIER) cc_final: 0.9007 (tpp80) REVERT: F 88 TYR cc_start: 0.8925 (m-80) cc_final: 0.8463 (m-80) REVERT: D 59 LYS cc_start: 0.9596 (mmmm) cc_final: 0.9186 (tppp) REVERT: D 63 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8648 (mm-30) REVERT: D 85 ASP cc_start: 0.8943 (m-30) cc_final: 0.8688 (t0) REVERT: A 92 LEU cc_start: 0.9578 (tt) cc_final: 0.9311 (pp) REVERT: A 94 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8583 (mm-30) REVERT: A 97 GLU cc_start: 0.8868 (pp20) cc_final: 0.8658 (pp20) REVERT: A 129 ARG cc_start: 0.9238 (ttp-170) cc_final: 0.9017 (ttm110) REVERT: B 40 ARG cc_start: 0.9364 (tpp80) cc_final: 0.9121 (tpp80) REVERT: B 44 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8637 (tmtt) REVERT: B 66 ILE cc_start: 0.9584 (pt) cc_final: 0.8344 (pt) REVERT: B 67 ARG cc_start: 0.9684 (tpp-160) cc_final: 0.9369 (mmp80) outliers start: 21 outliers final: 15 residues processed: 167 average time/residue: 0.1271 time to fit residues: 28.4433 Evaluate side-chains 156 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 39 ARG 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 100 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR 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 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: 10.0000 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 108 ASN ** 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 ** 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 = 0.3427 r_free = 0.3427 target = 0.049766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.033943 restraints weight = 78989.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.034943 restraints weight = 45417.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035615 restraints weight = 32353.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036027 restraints weight = 26048.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.036291 restraints weight = 22754.487| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10551 Z= 0.330 Angle : 0.768 13.877 15181 Z= 0.430 Chirality : 0.044 0.272 1833 Planarity : 0.005 0.060 1279 Dihedral : 31.942 179.975 3121 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 8.99 % Allowed : 33.86 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.27), residues: 897 helix: 0.63 (0.23), residues: 470 sheet: 0.68 (0.50), residues: 124 loop : -1.21 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 45 TYR 0.020 0.002 TYR H 72 PHE 0.029 0.003 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00722 (10551) covalent geometry : angle 0.76850 (15181) hydrogen bonds : bond 0.08811 ( 651) hydrogen bonds : angle 4.34693 ( 1667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 128 ARG cc_start: 0.9498 (tpp80) cc_final: 0.8980 (mmm160) REVERT: G 129 ARG cc_start: 0.9731 (ttt-90) cc_final: 0.9334 (mmm160) REVERT: H 92 ARG cc_start: 0.9186 (mtp-110) cc_final: 0.8731 (ttp80) REVERT: E 90 MET cc_start: 0.9222 (mmm) cc_final: 0.8997 (mmm) REVERT: F 88 TYR cc_start: 0.8992 (m-80) cc_final: 0.8391 (m-80) REVERT: C 50 GLU cc_start: 0.8995 (pt0) cc_final: 0.8463 (pt0) REVERT: C 54 TYR cc_start: 0.9264 (m-80) cc_final: 0.9055 (m-80) REVERT: C 120 MET cc_start: 0.7599 (mpp) cc_final: 0.7399 (mpp) REVERT: D 53 GLU cc_start: 0.9381 (tm-30) cc_final: 0.9165 (tm-30) REVERT: D 59 LYS cc_start: 0.9694 (mmmm) cc_final: 0.9231 (tppp) REVERT: D 60 VAL cc_start: 0.9710 (m) cc_final: 0.9475 (p) REVERT: D 63 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8849 (mm-30) REVERT: D 64 ASN cc_start: 0.9288 (m110) cc_final: 0.9041 (m110) REVERT: D 85 ASP cc_start: 0.8893 (m-30) cc_final: 0.8643 (t0) REVERT: A 90 MET cc_start: 0.8497 (tmt) cc_final: 0.7651 (tmm) REVERT: A 94 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8528 (mm-30) REVERT: A 120 MET cc_start: 0.8839 (mtt) cc_final: 0.8599 (mtt) REVERT: A 129 ARG cc_start: 0.9296 (ttp-170) cc_final: 0.9088 (ttm110) REVERT: B 40 ARG cc_start: 0.9375 (tpp80) cc_final: 0.9136 (tpp80) REVERT: B 62 LEU cc_start: 0.9725 (mm) cc_final: 0.9514 (mm) REVERT: B 66 ILE cc_start: 0.9707 (pt) cc_final: 0.8565 (pt) REVERT: B 67 ARG cc_start: 0.9702 (tpp-160) cc_final: 0.9416 (mmp80) outliers start: 34 outliers final: 22 residues processed: 163 average time/residue: 0.1302 time to fit residues: 28.2120 Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 49 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 60 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 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 D residue 51 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 97 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 49 LEU 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: 9.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.033939 restraints weight = 79999.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.034976 restraints weight = 44867.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035652 restraints weight = 31489.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.035903 restraints weight = 25112.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036303 restraints weight = 22492.907| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10551 Z= 0.291 Angle : 0.748 11.610 15181 Z= 0.416 Chirality : 0.042 0.200 1833 Planarity : 0.005 0.066 1279 Dihedral : 32.058 178.606 3121 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.67 % Allowed : 40.48 % Favored : 51.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.27), residues: 897 helix: 0.60 (0.23), residues: 472 sheet: 0.58 (0.50), residues: 123 loop : -1.36 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 55 TYR 0.016 0.001 TYR H 72 PHE 0.022 0.002 PHE C 84 TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00638 (10551) covalent geometry : angle 0.74848 (15181) hydrogen bonds : bond 0.07113 ( 651) hydrogen bonds : angle 4.10961 ( 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 173 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.302 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 128 ARG cc_start: 0.9483 (tpp80) cc_final: 0.9122 (mmm160) REVERT: G 129 ARG cc_start: 0.9737 (ttt-90) cc_final: 0.9320 (mmm160) REVERT: H 92 ARG cc_start: 0.9137 (mtp-110) cc_final: 0.8745 (ttp80) REVERT: H 93 GLN cc_start: 0.9565 (tp40) cc_final: 0.9083 (tm-30) REVERT: E 90 MET cc_start: 0.9212 (mmm) cc_final: 0.8982 (mmm) REVERT: E 97 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8615 (mm-30) REVERT: E 120 MET cc_start: 0.9380 (tpp) cc_final: 0.8720 (mmm) REVERT: F 88 TYR cc_start: 0.9068 (m-80) cc_final: 0.8517 (m-80) REVERT: C 90 MET cc_start: 0.9208 (tpp) cc_final: 0.8989 (tpp) REVERT: C 120 MET cc_start: 0.7667 (mpp) cc_final: 0.7330 (mpp) REVERT: D 53 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9199 (tm-30) REVERT: D 59 LYS cc_start: 0.9658 (mmmm) cc_final: 0.9159 (tppp) REVERT: D 63 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8889 (mm-30) REVERT: D 85 ASP cc_start: 0.8953 (m-30) cc_final: 0.8615 (t0) REVERT: A 94 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8686 (mm-30) REVERT: A 129 ARG cc_start: 0.9311 (ttp-170) cc_final: 0.9098 (ttm110) REVERT: B 44 LYS cc_start: 0.9310 (mmmt) cc_final: 0.8824 (tmtt) REVERT: B 67 ARG cc_start: 0.9681 (tpp-160) cc_final: 0.9441 (tpp80) REVERT: B 85 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7967 (m-30) outliers start: 29 outliers final: 22 residues processed: 163 average time/residue: 0.1225 time to fit residues: 26.8941 Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR 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 85 ASP Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.051350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035956 restraints weight = 75013.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.037044 restraints weight = 42263.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.037739 restraints weight = 29381.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.038222 restraints weight = 23312.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.038391 restraints weight = 19997.312| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10551 Z= 0.182 Angle : 0.719 10.768 15181 Z= 0.391 Chirality : 0.041 0.190 1833 Planarity : 0.004 0.043 1279 Dihedral : 31.802 179.426 3121 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 7.41 % Allowed : 42.33 % 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 aren not related in a simple way. whole: 0.14 (0.27), residues: 897 helix: 0.84 (0.23), residues: 471 sheet: 0.61 (0.49), residues: 123 loop : -1.26 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.016 0.001 TYR H 72 PHE 0.034 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00409 (10551) covalent geometry : angle 0.71869 (15181) hydrogen bonds : bond 0.05400 ( 651) hydrogen bonds : angle 3.83521 ( 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: 28 poor density : 146 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 PHE cc_start: 0.9780 (m-10) cc_final: 0.9454 (m-80) REVERT: G 129 ARG cc_start: 0.9751 (ttt-90) cc_final: 0.9449 (mmm-85) REVERT: H 92 ARG cc_start: 0.9105 (mtp-110) cc_final: 0.8855 (ttp80) REVERT: H 93 GLN cc_start: 0.9545 (tp40) cc_final: 0.9135 (tm-30) REVERT: E 90 MET cc_start: 0.9261 (mmm) cc_final: 0.9047 (mmm) REVERT: E 97 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8613 (mm-30) REVERT: E 120 MET cc_start: 0.9330 (tpp) cc_final: 0.9006 (tpp) REVERT: F 39 ARG cc_start: 0.9652 (OUTLIER) cc_final: 0.9285 (tpp80) REVERT: F 53 GLU cc_start: 0.9165 (tt0) cc_final: 0.8921 (tt0) REVERT: F 88 TYR cc_start: 0.9036 (m-80) cc_final: 0.8446 (m-80) REVERT: C 50 GLU cc_start: 0.8703 (pt0) cc_final: 0.8499 (pm20) REVERT: C 54 TYR cc_start: 0.9324 (m-80) cc_final: 0.8823 (m-80) REVERT: C 55 GLN cc_start: 0.8542 (mt0) cc_final: 0.8221 (mp10) REVERT: C 90 MET cc_start: 0.9132 (tpp) cc_final: 0.8556 (tpp) REVERT: C 94 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9030 (mm-30) REVERT: C 120 MET cc_start: 0.7641 (mpp) cc_final: 0.7262 (mpp) REVERT: C 125 GLN cc_start: 0.9459 (OUTLIER) cc_final: 0.9247 (pm20) REVERT: D 53 GLU cc_start: 0.9344 (tm-30) cc_final: 0.9104 (tm-30) REVERT: D 59 LYS cc_start: 0.9659 (mmmm) cc_final: 0.9105 (tppp) REVERT: D 63 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8902 (mm-30) REVERT: D 75 HIS cc_start: 0.9366 (t-90) cc_final: 0.9085 (m-70) REVERT: D 85 ASP cc_start: 0.8960 (m-30) cc_final: 0.8622 (t0) REVERT: A 90 MET cc_start: 0.8462 (tmt) cc_final: 0.7436 (tmm) REVERT: A 94 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8504 (mm-30) REVERT: A 97 GLU cc_start: 0.8989 (pp20) cc_final: 0.8772 (pp20) REVERT: A 120 MET cc_start: 0.8856 (mtt) cc_final: 0.8329 (mpp) REVERT: A 129 ARG cc_start: 0.9332 (ttp-170) cc_final: 0.9065 (ttm110) REVERT: B 40 ARG cc_start: 0.9370 (tpp80) cc_final: 0.9153 (tpp80) REVERT: B 67 ARG cc_start: 0.9682 (tpp-160) cc_final: 0.9379 (mmm160) REVERT: B 85 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8038 (m-30) outliers start: 28 outliers final: 20 residues processed: 164 average time/residue: 0.1168 time to fit residues: 26.1259 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 : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 51 TYR 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 85 ASP 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: 0.9990 chunk 77 optimal weight: 50.0000 chunk 2 optimal weight: 50.0000 chunk 104 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 51 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 36 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.048033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.032399 restraints weight = 80557.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.033364 restraints weight = 46300.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.033989 restraints weight = 33032.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.034214 restraints weight = 26750.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.034585 restraints weight = 24120.006| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 10551 Z= 0.329 Angle : 0.772 10.171 15181 Z= 0.433 Chirality : 0.043 0.267 1833 Planarity : 0.005 0.053 1279 Dihedral : 32.158 178.609 3121 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 7.67 % Allowed : 42.06 % 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 aren not related in a simple way. whole: -0.05 (0.27), residues: 897 helix: 0.64 (0.23), residues: 473 sheet: 0.58 (0.48), residues: 117 loop : -1.26 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.016 0.002 TYR D 51 PHE 0.043 0.003 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00720 (10551) covalent geometry : angle 0.77166 (15181) hydrogen bonds : bond 0.08844 ( 651) hydrogen bonds : angle 4.25929 ( 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 168 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 129 ARG cc_start: 0.9732 (ttt-90) cc_final: 0.9326 (mmm160) REVERT: H 92 ARG cc_start: 0.9073 (mtp-110) cc_final: 0.8782 (ttp80) REVERT: H 93 GLN cc_start: 0.9555 (tp40) cc_final: 0.9318 (tp-100) REVERT: E 90 MET cc_start: 0.9261 (mmm) cc_final: 0.9036 (mmm) REVERT: E 97 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8583 (mm-30) REVERT: F 39 ARG cc_start: 0.9613 (OUTLIER) cc_final: 0.9255 (tpp80) REVERT: F 88 TYR cc_start: 0.9044 (m-80) cc_final: 0.8429 (m-80) REVERT: C 50 GLU cc_start: 0.8810 (pt0) cc_final: 0.8423 (pm20) REVERT: C 54 TYR cc_start: 0.9324 (m-80) cc_final: 0.8866 (m-80) REVERT: C 55 GLN cc_start: 0.8589 (mt0) cc_final: 0.8315 (mp10) REVERT: C 90 MET cc_start: 0.9182 (tpp) cc_final: 0.8671 (tpp) REVERT: C 94 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9038 (mm-30) REVERT: C 120 MET cc_start: 0.7670 (mpp) cc_final: 0.7263 (mpp) REVERT: D 53 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9171 (tm-30) REVERT: D 59 LYS cc_start: 0.9668 (mmmm) cc_final: 0.9121 (tppp) REVERT: D 63 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8915 (mm-30) REVERT: D 64 ASN cc_start: 0.9278 (m110) cc_final: 0.9073 (m110) REVERT: D 75 HIS cc_start: 0.9383 (t-90) cc_final: 0.9103 (m-70) REVERT: A 90 MET cc_start: 0.8483 (tmt) cc_final: 0.7523 (tmm) REVERT: A 94 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 129 ARG cc_start: 0.9317 (ttp-170) cc_final: 0.9058 (ttm110) REVERT: B 40 ARG cc_start: 0.9427 (tpp80) cc_final: 0.9203 (tpp80) REVERT: B 53 GLU cc_start: 0.9587 (tp30) cc_final: 0.9307 (tp30) REVERT: B 67 ARG cc_start: 0.9682 (tpp-160) cc_final: 0.9471 (tpp80) outliers start: 29 outliers final: 26 residues processed: 156 average time/residue: 0.1119 time to fit residues: 24.2479 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 125 GLN 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 D residue 51 TYR 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 49 LEU Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 50.0000 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035670 restraints weight = 75410.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036758 restraints weight = 43217.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037473 restraints weight = 30289.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037941 restraints weight = 23947.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.038247 restraints weight = 20542.587| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10551 Z= 0.171 Angle : 0.745 12.596 15181 Z= 0.399 Chirality : 0.042 0.367 1833 Planarity : 0.004 0.045 1279 Dihedral : 31.742 179.447 3121 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 6.35 % Allowed : 46.03 % Favored : 47.62 % 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 aren not related in a simple way. whole: 0.18 (0.27), residues: 897 helix: 0.81 (0.23), residues: 475 sheet: 0.69 (0.48), residues: 117 loop : -1.13 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.016 0.001 TYR H 72 PHE 0.039 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (10551) covalent geometry : angle 0.74479 (15181) hydrogen bonds : bond 0.05220 ( 651) hydrogen bonds : angle 3.82735 ( 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 172 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.295 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: 0.9163 (OUTLIER) cc_final: 0.8664 (ttt-90) REVERT: G 129 ARG cc_start: 0.9747 (ttt-90) cc_final: 0.9456 (mmm-85) REVERT: H 93 GLN cc_start: 0.9518 (tp40) cc_final: 0.8936 (tp-100) REVERT: E 90 MET cc_start: 0.9304 (mmm) cc_final: 0.9062 (mmm) REVERT: E 97 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8637 (mm-30) REVERT: F 39 ARG cc_start: 0.9644 (OUTLIER) cc_final: 0.9262 (tpp80) REVERT: F 88 TYR cc_start: 0.8998 (m-80) cc_final: 0.8282 (m-80) REVERT: C 54 TYR cc_start: 0.9335 (m-80) cc_final: 0.9113 (m-80) REVERT: C 86 SER cc_start: 0.9707 (t) cc_final: 0.9483 (p) REVERT: C 90 MET cc_start: 0.9143 (tpp) cc_final: 0.8474 (tpp) REVERT: C 94 GLU cc_start: 0.9442 (mm-30) cc_final: 0.8981 (mm-30) REVERT: C 120 MET cc_start: 0.7671 (mpp) cc_final: 0.7251 (mpp) REVERT: D 53 GLU cc_start: 0.9377 (tm-30) cc_final: 0.9107 (tm-30) REVERT: D 59 LYS cc_start: 0.9663 (mmmm) cc_final: 0.9101 (tppp) REVERT: D 63 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8929 (mm-30) REVERT: D 64 ASN cc_start: 0.9235 (m110) cc_final: 0.9030 (m-40) REVERT: D 75 HIS cc_start: 0.9355 (t-90) cc_final: 0.9065 (m-70) REVERT: D 85 ASP cc_start: 0.8894 (m-30) cc_final: 0.8685 (t0) REVERT: A 94 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8641 (mm-30) REVERT: A 97 GLU cc_start: 0.8962 (pp20) cc_final: 0.8745 (pp20) REVERT: A 120 MET cc_start: 0.8876 (mtt) cc_final: 0.8344 (mpp) REVERT: A 129 ARG cc_start: 0.9355 (ttp-170) cc_final: 0.9028 (ttm110) REVERT: B 40 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9229 (tpp80) REVERT: B 67 ARG cc_start: 0.9685 (tpp-160) cc_final: 0.9463 (tpp80) outliers start: 24 outliers final: 16 residues processed: 163 average time/residue: 0.1147 time to fit residues: 25.7864 Evaluate side-chains 159 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR 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 B residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 50.0000 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 30.0000 chunk 34 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.035423 restraints weight = 76756.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.036502 restraints weight = 43128.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037184 restraints weight = 30084.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.037650 restraints weight = 23947.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.037947 restraints weight = 20631.204| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10551 Z= 0.187 Angle : 0.773 16.313 15181 Z= 0.413 Chirality : 0.042 0.368 1833 Planarity : 0.004 0.053 1279 Dihedral : 31.694 177.845 3121 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.56 % Allowed : 46.83 % Favored : 47.62 % 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 aren not related in a simple way. whole: 0.21 (0.27), residues: 897 helix: 0.83 (0.23), residues: 474 sheet: 0.70 (0.46), residues: 122 loop : -1.13 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.016 0.001 TYR H 72 PHE 0.053 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00420 (10551) covalent geometry : angle 0.77330 (15181) hydrogen bonds : bond 0.05449 ( 651) hydrogen bonds : angle 3.88718 ( 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: 21 poor density : 144 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8666 (ttt-90) REVERT: G 129 ARG cc_start: 0.9732 (ttt-90) cc_final: 0.9440 (mmm-85) REVERT: H 93 GLN cc_start: 0.9519 (tp40) cc_final: 0.8929 (tp-100) REVERT: E 90 MET cc_start: 0.9274 (mmm) cc_final: 0.9024 (mmm) REVERT: E 97 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8645 (mm-30) REVERT: E 120 MET cc_start: 0.9103 (mmm) cc_final: 0.8228 (mmt) REVERT: F 39 ARG cc_start: 0.9647 (tpp80) cc_final: 0.9271 (tpp80) REVERT: F 88 TYR cc_start: 0.8988 (m-80) cc_final: 0.8325 (m-80) REVERT: C 54 TYR cc_start: 0.9345 (m-80) cc_final: 0.9077 (m-80) REVERT: C 86 SER cc_start: 0.9705 (t) cc_final: 0.9480 (p) REVERT: C 90 MET cc_start: 0.9129 (tpp) cc_final: 0.8484 (tpp) REVERT: C 94 GLU cc_start: 0.9430 (mm-30) cc_final: 0.8989 (mm-30) REVERT: C 120 MET cc_start: 0.7687 (mpp) cc_final: 0.7299 (mpp) REVERT: D 53 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9104 (tm-30) REVERT: D 59 LYS cc_start: 0.9669 (mmmm) cc_final: 0.9086 (tppp) REVERT: D 63 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8919 (mm-30) REVERT: D 64 ASN cc_start: 0.9253 (m110) cc_final: 0.9021 (m110) REVERT: D 75 HIS cc_start: 0.9347 (t-90) cc_final: 0.9089 (m-70) REVERT: A 90 MET cc_start: 0.8456 (tmt) cc_final: 0.7736 (tmm) REVERT: A 94 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8485 (mm-30) REVERT: A 97 GLU cc_start: 0.8938 (pp20) cc_final: 0.8715 (pp20) REVERT: A 120 MET cc_start: 0.8851 (mtt) cc_final: 0.8320 (mpp) REVERT: A 129 ARG cc_start: 0.9340 (ttp-170) cc_final: 0.9016 (ttm110) REVERT: B 40 ARG cc_start: 0.9424 (tpp80) cc_final: 0.9213 (tpp80) REVERT: B 67 ARG cc_start: 0.9687 (tpp-160) cc_final: 0.9462 (tpp80) outliers start: 21 outliers final: 19 residues processed: 160 average time/residue: 0.1136 time to fit residues: 25.1978 Evaluate side-chains 158 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR 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 B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 chunk 106 optimal weight: 50.0000 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.048490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.032899 restraints weight = 78930.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.033873 restraints weight = 44733.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.034520 restraints weight = 31467.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.034941 restraints weight = 25292.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035187 restraints weight = 21942.613| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 10551 Z= 0.296 Angle : 0.818 13.590 15181 Z= 0.449 Chirality : 0.044 0.344 1833 Planarity : 0.005 0.059 1279 Dihedral : 32.034 177.481 3121 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 6.35 % Allowed : 46.03 % Favored : 47.62 % 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 aren not related in a simple way. whole: 0.08 (0.27), residues: 897 helix: 0.67 (0.23), residues: 476 sheet: 0.73 (0.47), residues: 117 loop : -1.11 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.015 0.001 TYR H 72 PHE 0.053 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 covalent geometry : bond 0.00660 (10551) covalent geometry : angle 0.81787 (15181) hydrogen bonds : bond 0.07685 ( 651) hydrogen bonds : angle 4.29380 ( 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 159 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 104 PHE cc_start: 0.9776 (m-10) cc_final: 0.9470 (m-80) REVERT: G 129 ARG cc_start: 0.9733 (ttt-90) cc_final: 0.9480 (mmm-85) REVERT: H 93 GLN cc_start: 0.9535 (tp40) cc_final: 0.8935 (tp-100) REVERT: E 97 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8718 (mm-30) REVERT: E 120 MET cc_start: 0.9130 (mmm) cc_final: 0.8759 (mmm) REVERT: F 39 ARG cc_start: 0.9640 (tpp80) cc_final: 0.9335 (tpp80) REVERT: F 88 TYR cc_start: 0.9014 (m-80) cc_final: 0.8357 (m-80) REVERT: C 54 TYR cc_start: 0.9384 (m-80) cc_final: 0.9140 (m-80) REVERT: C 90 MET cc_start: 0.9182 (tpp) cc_final: 0.8631 (tpp) REVERT: C 94 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9033 (mm-30) REVERT: C 120 MET cc_start: 0.7808 (mpp) cc_final: 0.7412 (mpp) REVERT: D 59 LYS cc_start: 0.9660 (mmmm) cc_final: 0.9082 (tppp) REVERT: D 63 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8887 (mm-30) REVERT: D 64 ASN cc_start: 0.9279 (m110) cc_final: 0.9040 (m110) REVERT: D 75 HIS cc_start: 0.9378 (t-90) cc_final: 0.9125 (m-70) REVERT: A 90 MET cc_start: 0.8471 (tmt) cc_final: 0.7703 (tmm) REVERT: A 94 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8504 (mm-30) REVERT: A 97 GLU cc_start: 0.8964 (pp20) cc_final: 0.8744 (pp20) REVERT: A 129 ARG cc_start: 0.9354 (ttp-170) cc_final: 0.9065 (ttm110) REVERT: B 40 ARG cc_start: 0.9410 (tpp80) cc_final: 0.9202 (tpp80) REVERT: B 53 GLU cc_start: 0.9564 (tp30) cc_final: 0.9312 (tp30) REVERT: B 67 ARG cc_start: 0.9690 (tpp-160) cc_final: 0.9485 (tpp80) outliers start: 24 outliers final: 22 residues processed: 151 average time/residue: 0.1107 time to fit residues: 23.1824 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 : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 THR 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 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: 7.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 52 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 30.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.048944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.033406 restraints weight = 77949.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.034390 restraints weight = 44048.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035050 restraints weight = 31012.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.035422 restraints weight = 24799.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035723 restraints weight = 21745.360| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 10551 Z= 0.255 Angle : 0.811 13.028 15181 Z= 0.439 Chirality : 0.043 0.364 1833 Planarity : 0.004 0.050 1279 Dihedral : 32.115 178.813 3121 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.61 % Allowed : 46.83 % Favored : 46.56 % 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 aren not related in a simple way. whole: 0.07 (0.27), residues: 897 helix: 0.63 (0.23), residues: 476 sheet: 0.72 (0.47), residues: 117 loop : -1.05 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.015 0.001 TYR H 72 PHE 0.052 0.002 PHE A 67 TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00570 (10551) covalent geometry : angle 0.81087 (15181) hydrogen bonds : bond 0.06504 ( 651) hydrogen bonds : angle 4.24456 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.87 seconds wall clock time: 39 minutes 23.08 seconds (2363.08 seconds total)