Starting phenix.real_space_refine on Tue May 13 23:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6s_36013/05_2025/8j6s_36013.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6s_36013/05_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_36013/05_2025/8j6s_36013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6s_36013/05_2025/8j6s_36013.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6s_36013/05_2025/8j6s_36013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6s_36013/05_2025/8j6s_36013.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 5, '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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLU:plan': 3, 'ARG: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, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP: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: {'GLN:plan1': 6, 'ARG:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 12, 'TRP:plan': 8, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 11, 'HIS:plan': 10} 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: 6.83, per 1000 atoms: 0.68 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: 2.99 Conformation dependent library (CDL) restraints added in 929.5 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 53.2% alpha, 12.3% beta 90 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 4.27 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: 4.37 Time building geometry restraints manager: 3.48 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 30.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.000 0.000 TRP L 10 HIS 0.013 0.004 HIS D 75 PHE 0.022 0.002 PHE E 84 TYR 0.044 0.002 TYR H 72 ARG 0.015 0.001 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.16855 ( 651) hydrogen bonds : angle 6.28185 ( 1667) covalent geometry : bond 0.00416 (10551) covalent geometry : angle 0.79481 (15181) *********************** 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 : 0.783 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: 0.2823 time to fit residues: 72.7363 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 : 0.824 ------------------------------------------------------------------------------- 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 90 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.3980 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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** C 85 GLN 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 = 0.3509 r_free = 0.3509 target = 0.054148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.038156 restraints weight = 71339.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039246 restraints weight = 42029.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.039960 restraints weight = 30039.865| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10551 Z= 0.218 Angle : 0.713 8.596 15181 Z= 0.403 Chirality : 0.041 0.236 1833 Planarity : 0.005 0.069 1279 Dihedral : 31.489 179.352 3123 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 6.35 % Allowed : 34.13 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.27), residues: 897 helix: 0.55 (0.22), residues: 469 sheet: 0.92 (0.47), residues: 129 loop : -1.34 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.008 0.003 HIS C 113 PHE 0.015 0.002 PHE C 104 TYR 0.030 0.002 TYR H 72 ARG 0.021 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.06361 ( 651) hydrogen bonds : angle 4.33061 ( 1667) covalent geometry : bond 0.00476 (10551) covalent geometry : angle 0.71260 (15181) *********************** 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 185 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.763 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 104 PHE cc_start: 0.9775 (m-10) cc_final: 0.9573 (m-10) REVERT: G 128 ARG cc_start: 0.9548 (tpp80) cc_final: 0.9293 (mmm160) REVERT: G 129 ARG cc_start: 0.9699 (ttt-90) cc_final: 0.9375 (mmm160) REVERT: H 90 LEU cc_start: 0.9563 (mt) cc_final: 0.9333 (pp) REVERT: H 92 ARG cc_start: 0.9205 (mtp-110) cc_final: 0.8830 (ttp80) REVERT: H 93 GLN cc_start: 0.9516 (tp40) cc_final: 0.9051 (tm-30) REVERT: E 97 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8935 (mm-30) REVERT: E 131 ARG cc_start: 0.9440 (tpp80) cc_final: 0.9076 (mtp180) REVERT: F 88 TYR cc_start: 0.8858 (m-80) cc_final: 0.8519 (m-80) REVERT: D 59 LYS cc_start: 0.9643 (mmmm) cc_final: 0.9344 (tppp) REVERT: D 63 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8776 (mm-30) REVERT: A 90 MET cc_start: 0.8483 (tmt) cc_final: 0.7654 (tmm) REVERT: A 94 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8451 (mm-30) REVERT: A 106 ASP cc_start: 0.9411 (t70) cc_final: 0.9115 (t70) REVERT: A 129 ARG cc_start: 0.9268 (ttp-170) cc_final: 0.9061 (ttm110) outliers start: 24 outliers final: 11 residues processed: 178 average time/residue: 0.2388 time to fit residues: 57.1183 Evaluate side-chains 151 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 113 HIS 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 C residue 108 ASN 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 40 optimal weight: 7.9990 chunk 98 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.054285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.038376 restraints weight = 72807.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.039500 restraints weight = 41915.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040216 restraints weight = 29600.222| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10551 Z= 0.182 Angle : 0.691 12.119 15181 Z= 0.384 Chirality : 0.041 0.299 1833 Planarity : 0.005 0.051 1279 Dihedral : 31.409 178.980 3121 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.29 % Allowed : 37.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 897 helix: 0.79 (0.23), residues: 468 sheet: 0.91 (0.48), residues: 129 loop : -1.26 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.007 0.002 HIS C 113 PHE 0.018 0.001 PHE C 84 TYR 0.026 0.002 TYR H 72 ARG 0.010 0.001 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.05460 ( 651) hydrogen bonds : angle 3.99615 ( 1667) covalent geometry : bond 0.00402 (10551) covalent geometry : angle 0.69077 (15181) *********************** 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: 20 poor density : 154 time to evaluate : 0.761 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 119 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8939 (mp) REVERT: G 120 MET cc_start: 0.8999 (pmm) cc_final: 0.8797 (pmm) REVERT: G 128 ARG cc_start: 0.9528 (tpp80) cc_final: 0.8547 (mmm160) REVERT: G 129 ARG cc_start: 0.9714 (ttt-90) cc_final: 0.9352 (mmm160) REVERT: H 92 ARG cc_start: 0.9201 (mtp-110) cc_final: 0.8802 (ttp80) REVERT: E 51 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8155 (mm) REVERT: E 131 ARG cc_start: 0.9471 (tpp80) cc_final: 0.9260 (mtp180) REVERT: F 39 ARG cc_start: 0.9632 (OUTLIER) cc_final: 0.9292 (tpp80) REVERT: F 88 TYR cc_start: 0.8900 (m-80) cc_final: 0.8419 (m-80) REVERT: D 59 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9238 (tppp) REVERT: D 63 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8713 (mm-30) REVERT: D 67 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8894 (ttp80) REVERT: D 85 ASP cc_start: 0.8953 (m-30) cc_final: 0.8722 (t0) REVERT: A 90 MET cc_start: 0.8419 (tmt) cc_final: 0.7663 (tmm) REVERT: A 92 LEU cc_start: 0.9644 (tt) cc_final: 0.9350 (pp) REVERT: A 94 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8455 (mm-30) REVERT: A 97 GLU cc_start: 0.8885 (pp20) cc_final: 0.8644 (pp20) REVERT: A 129 ARG cc_start: 0.9316 (ttp-170) cc_final: 0.9042 (ttm110) REVERT: B 66 ILE cc_start: 0.9602 (pt) cc_final: 0.8376 (pt) REVERT: B 67 ARG cc_start: 0.9703 (tpp-160) cc_final: 0.9379 (mmp80) outliers start: 20 outliers final: 13 residues processed: 163 average time/residue: 0.2357 time to fit residues: 51.8476 Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain E residue 51 ILE 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 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 49 LEU 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 61 optimal weight: 0.3980 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 76 optimal weight: 50.0000 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN E 108 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.053990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038189 restraints weight = 72677.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.039306 restraints weight = 41735.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.040033 restraints weight = 29275.593| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10551 Z= 0.179 Angle : 0.693 13.430 15181 Z= 0.377 Chirality : 0.040 0.295 1833 Planarity : 0.004 0.049 1279 Dihedral : 31.359 179.365 3121 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.67 % Allowed : 35.71 % Favored : 56.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 897 helix: 0.97 (0.23), residues: 469 sheet: 0.90 (0.48), residues: 129 loop : -1.21 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS C 113 PHE 0.025 0.002 PHE A 67 TYR 0.021 0.001 TYR H 72 ARG 0.008 0.001 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.05386 ( 651) hydrogen bonds : angle 3.79839 ( 1667) covalent geometry : bond 0.00394 (10551) covalent geometry : angle 0.69277 (15181) *********************** 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: 29 poor density : 150 time to evaluate : 0.826 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: G 128 ARG cc_start: 0.9538 (tpp80) cc_final: 0.9143 (mmm160) REVERT: G 129 ARG cc_start: 0.9721 (ttt-90) cc_final: 0.9350 (mmm160) REVERT: H 92 ARG cc_start: 0.9178 (mtp-110) cc_final: 0.8755 (ttp80) REVERT: E 51 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8168 (mm) REVERT: E 97 GLU cc_start: 0.9348 (mm-30) cc_final: 0.8750 (mm-30) REVERT: E 125 GLN cc_start: 0.9558 (mm-40) cc_final: 0.9250 (mm-40) REVERT: E 131 ARG cc_start: 0.9473 (tpp80) cc_final: 0.9154 (mtp180) REVERT: F 39 ARG cc_start: 0.9651 (OUTLIER) cc_final: 0.9360 (tpp80) REVERT: F 88 TYR cc_start: 0.8917 (m-80) cc_final: 0.8368 (m-80) REVERT: D 59 LYS cc_start: 0.9611 (mmmm) cc_final: 0.9217 (tppp) REVERT: D 63 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8499 (mm-30) REVERT: D 64 ASN cc_start: 0.9290 (m110) cc_final: 0.8961 (m-40) REVERT: D 67 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8663 (ttm-80) REVERT: D 85 ASP cc_start: 0.8977 (m-30) cc_final: 0.8700 (t0) REVERT: A 90 MET cc_start: 0.8511 (tmt) cc_final: 0.7563 (tmm) REVERT: A 94 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8663 (mm-30) REVERT: B 55 ARG cc_start: 0.9443 (OUTLIER) cc_final: 0.9109 (mmt90) REVERT: B 62 LEU cc_start: 0.9706 (mm) cc_final: 0.9444 (mm) REVERT: B 66 ILE cc_start: 0.9601 (pt) cc_final: 0.8352 (pt) REVERT: B 67 ARG cc_start: 0.9699 (tpp-160) cc_final: 0.9370 (mmp80) outliers start: 29 outliers final: 18 residues processed: 167 average time/residue: 0.2677 time to fit residues: 58.6124 Evaluate side-chains 159 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 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 74 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG 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 52 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3497 r_free = 0.3497 target = 0.053266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037260 restraints weight = 76107.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038351 restraints weight = 43465.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039055 restraints weight = 30646.013| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10551 Z= 0.195 Angle : 0.693 10.740 15181 Z= 0.380 Chirality : 0.040 0.174 1833 Planarity : 0.005 0.048 1279 Dihedral : 31.421 178.639 3121 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 7.41 % Allowed : 36.51 % Favored : 56.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.27), residues: 897 helix: 0.99 (0.23), residues: 470 sheet: 0.86 (0.48), residues: 129 loop : -1.15 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS H 75 PHE 0.019 0.001 PHE C 84 TYR 0.019 0.001 TYR H 72 ARG 0.010 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05652 ( 651) hydrogen bonds : angle 3.74367 ( 1667) covalent geometry : bond 0.00432 (10551) covalent geometry : angle 0.69302 (15181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.855 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: G 128 ARG cc_start: 0.9486 (tpp80) cc_final: 0.9071 (mmm160) REVERT: G 129 ARG cc_start: 0.9715 (ttt-90) cc_final: 0.9361 (mmm160) REVERT: H 92 ARG cc_start: 0.9159 (mtp-110) cc_final: 0.8751 (ttp80) REVERT: E 51 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8170 (mm) REVERT: E 97 GLU cc_start: 0.9328 (mm-30) cc_final: 0.8677 (mm-30) REVERT: E 125 GLN cc_start: 0.9535 (mm-40) cc_final: 0.9230 (mm-40) REVERT: F 39 ARG cc_start: 0.9658 (OUTLIER) cc_final: 0.9381 (tpp80) REVERT: F 88 TYR cc_start: 0.8976 (m-80) cc_final: 0.8385 (m-80) REVERT: C 50 GLU cc_start: 0.8835 (pt0) cc_final: 0.8328 (pm20) REVERT: C 54 TYR cc_start: 0.9440 (m-80) cc_final: 0.8995 (m-80) REVERT: D 59 LYS cc_start: 0.9642 (mmmm) cc_final: 0.9180 (tppp) REVERT: D 63 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 64 ASN cc_start: 0.9348 (m110) cc_final: 0.9113 (m-40) REVERT: D 67 ARG cc_start: 0.9204 (ttp80) cc_final: 0.8645 (ttm-80) REVERT: D 85 ASP cc_start: 0.8981 (m-30) cc_final: 0.8676 (t0) REVERT: A 63 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.8085 (mmt90) REVERT: A 94 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8833 (mm-30) REVERT: A 120 MET cc_start: 0.8802 (mtt) cc_final: 0.8375 (mpp) REVERT: A 129 ARG cc_start: 0.9232 (ttm110) cc_final: 0.8739 (ptm160) REVERT: B 55 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9023 (ttm-80) REVERT: B 66 ILE cc_start: 0.9583 (pt) cc_final: 0.8267 (pt) REVERT: B 67 ARG cc_start: 0.9681 (tpp-160) cc_final: 0.9371 (mmp80) REVERT: B 85 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8071 (m-30) outliers start: 28 outliers final: 18 residues processed: 167 average time/residue: 0.2637 time to fit residues: 57.5681 Evaluate side-chains 162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain E residue 51 ILE 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 46 ILE 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 126 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 63 ARG 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 55 ARG 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 17 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 50.0000 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** C 68 GLN ** 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 = 0.3460 r_free = 0.3460 target = 0.051310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035615 restraints weight = 77775.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.036685 restraints weight = 43818.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.037380 restraints weight = 30629.577| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10551 Z= 0.244 Angle : 0.734 12.178 15181 Z= 0.400 Chirality : 0.042 0.279 1833 Planarity : 0.005 0.051 1279 Dihedral : 31.668 178.560 3121 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 8.20 % Allowed : 38.36 % Favored : 53.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 897 helix: 0.87 (0.23), residues: 469 sheet: 0.93 (0.49), residues: 122 loop : -1.10 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS G 113 PHE 0.023 0.002 PHE C 84 TYR 0.015 0.001 TYR H 72 ARG 0.010 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06766 ( 651) hydrogen bonds : angle 3.90874 ( 1667) covalent geometry : bond 0.00541 (10551) covalent geometry : angle 0.73369 (15181) *********************** 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 176 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.826 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: 0.9212 (OUTLIER) cc_final: 0.8701 (ttt-90) REVERT: G 100 LEU cc_start: 0.9740 (pp) cc_final: 0.9469 (pp) REVERT: G 104 PHE cc_start: 0.9812 (m-10) cc_final: 0.9566 (m-80) REVERT: G 128 ARG cc_start: 0.9471 (tpp80) cc_final: 0.9021 (mmm160) REVERT: G 129 ARG cc_start: 0.9730 (ttt-90) cc_final: 0.9356 (mmm160) REVERT: H 45 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7622 (tpp-160) REVERT: H 92 ARG cc_start: 0.9133 (mtp-110) cc_final: 0.8860 (ttp80) REVERT: H 93 GLN cc_start: 0.9545 (tp40) cc_final: 0.9158 (tm-30) REVERT: E 97 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8615 (mm-30) REVERT: E 125 GLN cc_start: 0.9547 (mm-40) cc_final: 0.9246 (mm-40) REVERT: F 39 ARG cc_start: 0.9655 (tpp80) cc_final: 0.9365 (tpp80) REVERT: F 53 GLU cc_start: 0.9264 (tt0) cc_final: 0.8348 (tt0) REVERT: F 88 TYR cc_start: 0.9043 (m-80) cc_final: 0.8547 (m-80) REVERT: C 55 GLN cc_start: 0.8440 (mt0) cc_final: 0.8188 (mp10) REVERT: D 59 LYS cc_start: 0.9692 (mmmm) cc_final: 0.9178 (tppp) REVERT: D 63 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8413 (mm-30) REVERT: D 64 ASN cc_start: 0.9376 (m110) cc_final: 0.8853 (m110) REVERT: D 67 ARG cc_start: 0.9212 (ttp80) cc_final: 0.8641 (ttm-80) REVERT: D 75 HIS cc_start: 0.9344 (t-90) cc_final: 0.9045 (m-70) REVERT: D 85 ASP cc_start: 0.8950 (m-30) cc_final: 0.8616 (t0) REVERT: A 90 MET cc_start: 0.8575 (tmt) cc_final: 0.7658 (tmm) REVERT: A 94 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8742 (mm-30) REVERT: B 55 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.8928 (mmt90) REVERT: B 66 ILE cc_start: 0.9658 (pt) cc_final: 0.8527 (pt) REVERT: B 67 ARG cc_start: 0.9684 (tpp-160) cc_final: 0.9401 (mmp80) REVERT: B 85 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8074 (m-30) outliers start: 31 outliers final: 20 residues processed: 165 average time/residue: 0.2586 time to fit residues: 56.4115 Evaluate side-chains 162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain H residue 45 ARG Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 46 ILE 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 126 LEU Chi-restraints excluded: chain D residue 50 ILE 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 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 87 optimal weight: 10.0000 chunk 77 optimal weight: 50.0000 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** C 68 GLN ** 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 = 0.3468 r_free = 0.3468 target = 0.051651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.035571 restraints weight = 76939.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036644 restraints weight = 43653.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.037357 restraints weight = 30661.066| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10551 Z= 0.208 Angle : 0.732 13.268 15181 Z= 0.394 Chirality : 0.041 0.346 1833 Planarity : 0.004 0.046 1279 Dihedral : 31.614 178.085 3121 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 8.73 % Allowed : 39.95 % Favored : 51.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 897 helix: 1.10 (0.23), residues: 467 sheet: 1.05 (0.49), residues: 117 loop : -0.97 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS G 113 PHE 0.020 0.002 PHE C 84 TYR 0.016 0.001 TYR H 72 ARG 0.013 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05631 ( 651) hydrogen bonds : angle 3.79148 ( 1667) covalent geometry : bond 0.00465 (10551) covalent geometry : angle 0.73237 (15181) *********************** 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 174 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.761 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: 0.9197 (OUTLIER) cc_final: 0.8719 (ttt-90) REVERT: G 128 ARG cc_start: 0.9483 (tpp80) cc_final: 0.9057 (mmm160) REVERT: G 129 ARG cc_start: 0.9747 (ttt-90) cc_final: 0.9346 (mmm160) REVERT: H 92 ARG cc_start: 0.9170 (mtp-110) cc_final: 0.8919 (ttp80) REVERT: H 93 GLN cc_start: 0.9525 (tp40) cc_final: 0.9152 (tm-30) REVERT: E 51 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8135 (mm) REVERT: E 97 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8687 (mm-30) REVERT: F 39 ARG cc_start: 0.9669 (OUTLIER) cc_final: 0.9350 (tpp80) REVERT: F 88 TYR cc_start: 0.9053 (m-80) cc_final: 0.8542 (m-80) REVERT: C 50 GLU cc_start: 0.8533 (pm20) cc_final: 0.7820 (pm20) REVERT: C 54 TYR cc_start: 0.9381 (m-80) cc_final: 0.9000 (m-80) REVERT: C 86 SER cc_start: 0.9705 (t) cc_final: 0.9464 (p) REVERT: D 59 LYS cc_start: 0.9681 (mmmm) cc_final: 0.8746 (tppp) REVERT: D 63 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8612 (mm-30) REVERT: D 64 ASN cc_start: 0.9402 (m110) cc_final: 0.8932 (m110) REVERT: D 67 ARG cc_start: 0.9188 (ttp80) cc_final: 0.8685 (ttm-80) REVERT: D 75 HIS cc_start: 0.9371 (t-90) cc_final: 0.9072 (m-70) REVERT: D 85 ASP cc_start: 0.8997 (m-30) cc_final: 0.8669 (t0) REVERT: A 90 MET cc_start: 0.8527 (tmt) cc_final: 0.7605 (tmm) REVERT: A 94 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 97 GLU cc_start: 0.9036 (pp20) cc_final: 0.8765 (pp20) REVERT: A 120 MET cc_start: 0.8903 (mtt) cc_final: 0.8381 (mpp) REVERT: A 129 ARG cc_start: 0.9279 (ttm110) cc_final: 0.8810 (ptm160) REVERT: B 55 ARG cc_start: 0.9417 (OUTLIER) cc_final: 0.8872 (mmt90) REVERT: B 67 ARG cc_start: 0.9682 (tpp-160) cc_final: 0.9455 (tpp80) REVERT: B 85 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8074 (m-30) outliers start: 33 outliers final: 26 residues processed: 163 average time/residue: 0.2616 time to fit residues: 57.1896 Evaluate side-chains 167 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER 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 118 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain 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 126 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL 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 2 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 82 optimal weight: 50.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.049356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.033838 restraints weight = 79621.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034847 restraints weight = 44761.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035549 restraints weight = 31395.882| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10551 Z= 0.291 Angle : 0.779 15.278 15181 Z= 0.425 Chirality : 0.043 0.416 1833 Planarity : 0.005 0.048 1279 Dihedral : 31.952 177.682 3121 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 9.52 % Allowed : 39.68 % Favored : 50.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 897 helix: 0.84 (0.23), residues: 470 sheet: 0.98 (0.49), residues: 117 loop : -1.04 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.004 0.002 HIS G 113 PHE 0.046 0.003 PHE A 67 TYR 0.014 0.001 TYR H 72 ARG 0.010 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.07797 ( 651) hydrogen bonds : angle 4.14389 ( 1667) covalent geometry : bond 0.00644 (10551) covalent geometry : angle 0.77907 (15181) *********************** 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 174 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.877 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 63 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8698 (ttt-90) REVERT: G 104 PHE cc_start: 0.9783 (m-10) cc_final: 0.9539 (m-80) REVERT: G 128 ARG cc_start: 0.9486 (tpp80) cc_final: 0.9011 (mmm160) REVERT: G 129 ARG cc_start: 0.9726 (ttt-90) cc_final: 0.9345 (mmm160) REVERT: H 92 ARG cc_start: 0.9104 (mtp-110) cc_final: 0.8817 (ttp80) REVERT: H 93 GLN cc_start: 0.9551 (tp40) cc_final: 0.9322 (tp-100) REVERT: F 39 ARG cc_start: 0.9657 (OUTLIER) cc_final: 0.9281 (tpp80) REVERT: F 88 TYR cc_start: 0.9022 (m-80) cc_final: 0.8402 (m-80) REVERT: D 59 LYS cc_start: 0.9682 (mmmm) cc_final: 0.9127 (tppp) REVERT: D 63 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8572 (mm-30) REVERT: D 64 ASN cc_start: 0.9431 (m110) cc_final: 0.8952 (m110) REVERT: D 67 ARG cc_start: 0.9168 (ttp80) cc_final: 0.8606 (ttm-80) REVERT: D 75 HIS cc_start: 0.9386 (t-90) cc_final: 0.9107 (m-70) REVERT: A 90 MET cc_start: 0.8522 (tmt) cc_final: 0.7615 (tmm) REVERT: A 94 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8734 (mm-30) REVERT: A 120 MET cc_start: 0.8939 (mtt) cc_final: 0.8372 (mpp) REVERT: B 67 ARG cc_start: 0.9698 (tpp-160) cc_final: 0.9402 (mmp80) outliers start: 36 outliers final: 32 residues processed: 160 average time/residue: 0.2510 time to fit residues: 53.9441 Evaluate side-chains 164 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain E residue 57 SER 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 110 CYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 LEU 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 D residue 97 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 99 optimal weight: 0.0980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.051687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.035555 restraints weight = 75518.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.036635 restraints weight = 42864.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037338 restraints weight = 30103.896| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10551 Z= 0.178 Angle : 0.784 15.962 15181 Z= 0.411 Chirality : 0.043 0.448 1833 Planarity : 0.004 0.055 1279 Dihedral : 31.722 177.132 3121 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.61 % Allowed : 43.92 % Favored : 49.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 897 helix: 0.86 (0.23), residues: 474 sheet: 0.97 (0.47), residues: 122 loop : -0.91 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.006 0.002 HIS G 113 PHE 0.025 0.001 PHE A 67 TYR 0.016 0.001 TYR H 72 ARG 0.013 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 651) hydrogen bonds : angle 3.84175 ( 1667) covalent geometry : bond 0.00399 (10551) covalent geometry : angle 0.78383 (15181) *********************** 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 168 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.764 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: 0.9150 (OUTLIER) cc_final: 0.8690 (ttt-90) REVERT: G 129 ARG cc_start: 0.9758 (ttt-90) cc_final: 0.9496 (mmm-85) REVERT: H 93 GLN cc_start: 0.9511 (tp40) cc_final: 0.8938 (tp-100) REVERT: E 97 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8707 (mm-30) REVERT: F 88 TYR cc_start: 0.8965 (m-80) cc_final: 0.8354 (m-80) REVERT: C 54 TYR cc_start: 0.9286 (m-80) cc_final: 0.8773 (m-80) REVERT: C 86 SER cc_start: 0.9703 (t) cc_final: 0.9468 (p) REVERT: D 39 ARG cc_start: 0.9537 (tpp-160) cc_final: 0.9214 (tpp80) REVERT: D 59 LYS cc_start: 0.9658 (mmmm) cc_final: 0.9082 (tppp) REVERT: D 63 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8637 (mm-30) REVERT: D 64 ASN cc_start: 0.9393 (m110) cc_final: 0.8919 (m110) REVERT: D 67 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8659 (ttm-80) REVERT: D 75 HIS cc_start: 0.9357 (t-90) cc_final: 0.9047 (m-70) REVERT: D 85 ASP cc_start: 0.8937 (m-30) cc_final: 0.8725 (t0) REVERT: A 90 MET cc_start: 0.8506 (tmt) cc_final: 0.7597 (tmm) REVERT: A 94 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8681 (mm-30) REVERT: A 97 GLU cc_start: 0.9013 (pp20) cc_final: 0.8755 (pp20) REVERT: A 120 MET cc_start: 0.8933 (mtt) cc_final: 0.8431 (mpp) REVERT: A 129 ARG cc_start: 0.9273 (ttm110) cc_final: 0.8800 (ptm160) REVERT: B 55 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8653 (ttm-80) REVERT: B 67 ARG cc_start: 0.9702 (tpp-160) cc_final: 0.9492 (tpp80) outliers start: 25 outliers final: 21 residues processed: 160 average time/residue: 0.2462 time to fit residues: 52.7365 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 46 ILE 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 100 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 0.0010 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** C 125 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 = 0.3445 r_free = 0.3445 target = 0.050326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.034626 restraints weight = 77073.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.035669 restraints weight = 43679.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036334 restraints weight = 30623.303| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 10551 Z= 0.232 Angle : 0.814 17.807 15181 Z= 0.428 Chirality : 0.042 0.462 1833 Planarity : 0.005 0.052 1279 Dihedral : 31.745 176.330 3121 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 7.14 % Allowed : 43.65 % Favored : 49.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 897 helix: 0.75 (0.23), residues: 475 sheet: 0.98 (0.47), residues: 122 loop : -0.93 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.020 0.001 PHE C 84 TYR 0.015 0.001 TYR H 72 ARG 0.013 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.06234 ( 651) hydrogen bonds : angle 4.01346 ( 1667) covalent geometry : bond 0.00519 (10551) covalent geometry : angle 0.81357 (15181) ********************** 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 161 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 63 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8685 (ttt-90) REVERT: G 129 ARG cc_start: 0.9752 (ttt-90) cc_final: 0.9463 (mmm-85) REVERT: H 92 ARG cc_start: 0.9155 (mtp-110) cc_final: 0.8872 (ttp80) REVERT: E 97 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8681 (mm-30) REVERT: E 120 MET cc_start: 0.9190 (mmm) cc_final: 0.8292 (mtt) REVERT: F 88 TYR cc_start: 0.8975 (m-80) cc_final: 0.8434 (m-80) REVERT: C 54 TYR cc_start: 0.9277 (m-80) cc_final: 0.8823 (m-80) REVERT: C 55 GLN cc_start: 0.8427 (mt0) cc_final: 0.8143 (mt0) REVERT: D 39 ARG cc_start: 0.9535 (tpp-160) cc_final: 0.9140 (tpp80) REVERT: D 59 LYS cc_start: 0.9666 (mmmm) cc_final: 0.9092 (tppp) REVERT: D 63 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8860 (mm-30) REVERT: D 64 ASN cc_start: 0.9409 (m110) cc_final: 0.8937 (m110) REVERT: D 67 ARG cc_start: 0.9114 (ttp80) cc_final: 0.8833 (ttm110) REVERT: D 75 HIS cc_start: 0.9379 (t-90) cc_final: 0.9074 (m-70) REVERT: D 85 ASP cc_start: 0.8969 (m-30) cc_final: 0.8732 (t0) REVERT: A 90 MET cc_start: 0.8484 (tmt) cc_final: 0.7643 (ppp) REVERT: A 94 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 97 GLU cc_start: 0.9004 (pp20) cc_final: 0.8749 (pp20) REVERT: A 120 MET cc_start: 0.8925 (mtt) cc_final: 0.8400 (mpp) REVERT: B 55 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.8789 (ttm-80) REVERT: B 67 ARG cc_start: 0.9697 (tpp-160) cc_final: 0.9496 (tpp80) outliers start: 27 outliers final: 24 residues processed: 154 average time/residue: 0.2316 time to fit residues: 48.2215 Evaluate side-chains 157 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 99 TYR Chi-restraints excluded: chain E residue 57 SER 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 118 THR Chi-restraints excluded: chain F residue 46 ILE 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 100 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 28 optimal weight: 0.2980 chunk 22 optimal weight: 0.0670 chunk 100 optimal weight: 50.0000 chunk 1 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 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 = 0.3477 r_free = 0.3477 target = 0.051753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.035995 restraints weight = 74133.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037078 restraints weight = 41718.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.037803 restraints weight = 29123.796| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10551 Z= 0.172 Angle : 0.807 16.966 15181 Z= 0.416 Chirality : 0.042 0.460 1833 Planarity : 0.004 0.058 1279 Dihedral : 31.623 175.464 3121 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.82 % Allowed : 44.97 % Favored : 49.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 897 helix: 0.80 (0.23), residues: 475 sheet: 1.09 (0.47), residues: 122 loop : -0.86 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 10 HIS 0.005 0.002 HIS G 113 PHE 0.013 0.001 PHE C 84 TYR 0.016 0.001 TYR H 72 ARG 0.014 0.001 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 651) hydrogen bonds : angle 3.81162 ( 1667) covalent geometry : bond 0.00388 (10551) covalent geometry : angle 0.80714 (15181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.99 seconds wall clock time: 63 minutes 3.92 seconds (3783.92 seconds total)