Starting phenix.real_space_refine on Thu Sep 18 09:22:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.map" model { file = "/net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2m_53532/09_2025/9r2m_53532.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 286 5.49 5 S 14 5.16 5 C 9050 2.51 5 N 3043 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15971 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 765 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2912 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2951 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "L" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "M" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Chain: "N" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1017 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 14, 'TRANS': 185} Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'PHE:plan': 5, 'ARG:plan': 18, 'HIS:plan': 7, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 11} Unresolved non-hydrogen planarities: 343 Time building chain proxies: 4.46, per 1000 atoms: 0.28 Number of scatterers: 15971 At special positions: 0 Unit cell: (121.684, 182.525, 138.584, 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 14 16.00 P 286 15.00 O 3578 8.00 N 3043 7.00 C 9050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 659.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2914 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 18 sheets defined 41.8% alpha, 15.0% beta 125 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.662A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.520A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 removed outlier: 3.682A pdb=" N VAL C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.362A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.526A pdb=" N LYS D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.527A pdb=" N ARG D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.537A pdb=" N ILE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.527A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 Processing helix chain 'F' and resid 31 through 42 removed outlier: 3.644A pdb=" N GLY F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.517A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.504A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 47 through 74 removed outlier: 3.599A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.674A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.509A pdb=" N LEU H 46 " --> pdb=" O VAL H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.570A pdb=" N ILE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'K' and resid 165 through 169 Processing helix chain 'K' and resid 176 through 182 Processing helix chain 'K' and resid 277 through 291 removed outlier: 3.807A pdb=" N ASP K 281 " --> pdb=" O CYS K 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 4.150A pdb=" N TYR L 107 " --> pdb=" O GLN L 104 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY L 108 " --> pdb=" O GLY L 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 104 through 108' Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 277 through 291 Processing helix chain 'M' and resid 165 through 169 removed outlier: 3.547A pdb=" N MET M 169 " --> pdb=" O SER M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 182 removed outlier: 3.562A pdb=" N ARG M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 277 through 290 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 182 Processing helix chain 'N' and resid 277 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.977A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.347A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.521A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.968A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.290A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127 removed outlier: 3.637A pdb=" N CYS K 135 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL K 272 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE K 251 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA K 161 " --> pdb=" O HIS K 214 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS K 214 " --> pdb=" O ALA K 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112 Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127 removed outlier: 6.299A pdb=" N MET L 133 " --> pdb=" O ARG L 273 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE L 251 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ALA L 161 " --> pdb=" O HIS L 214 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS L 214 " --> pdb=" O ALA L 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112 removed outlier: 3.507A pdb=" N GLY M 112 " --> pdb=" O GLN M 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127 removed outlier: 4.169A pdb=" N ILE M 251 " --> pdb=" O VAL M 272 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA M 161 " --> pdb=" O HIS M 214 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS M 214 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112 Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127 removed outlier: 4.333A pdb=" N ILE N 251 " --> pdb=" O VAL N 272 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ALA N 161 " --> pdb=" O HIS N 214 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS N 214 " --> pdb=" O ALA N 161 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4011 1.33 - 1.45: 4058 1.45 - 1.57: 8157 1.57 - 1.69: 570 1.69 - 1.81: 24 Bond restraints: 16820 Sorted by residual: bond pdb=" C SER L 96 " pdb=" N VAL L 97 " ideal model delta sigma weight residual 1.334 1.324 0.009 1.06e-02 8.90e+03 7.99e-01 bond pdb=" N SER K 127 " pdb=" CA SER K 127 " ideal model delta sigma weight residual 1.463 1.454 0.010 1.08e-02 8.57e+03 7.74e-01 bond pdb=" N VAL L 97 " pdb=" CA VAL L 97 " ideal model delta sigma weight residual 1.454 1.461 -0.006 7.70e-03 1.69e+04 7.04e-01 bond pdb=" CA PRO K 190 " pdb=" C PRO K 190 " ideal model delta sigma weight residual 1.517 1.509 0.008 9.30e-03 1.16e+04 6.87e-01 bond pdb=" C3' DC I 80 " pdb=" C2' DC I 80 " ideal model delta sigma weight residual 1.525 1.540 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 16815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 22342 0.91 - 1.81: 1234 1.81 - 2.72: 454 2.72 - 3.63: 101 3.63 - 4.53: 16 Bond angle restraints: 24147 Sorted by residual: angle pdb=" N SER L 183 " pdb=" CA SER L 183 " pdb=" C SER L 183 " ideal model delta sigma weight residual 108.24 112.77 -4.53 1.81e+00 3.05e-01 6.27e+00 angle pdb=" N GLY G 38 " pdb=" CA GLY G 38 " pdb=" C GLY G 38 " ideal model delta sigma weight residual 115.36 112.22 3.14 1.33e+00 5.65e-01 5.56e+00 angle pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " pdb=" C1' DA I 90 " ideal model delta sigma weight residual 101.60 104.97 -3.37 1.50e+00 4.44e-01 5.04e+00 angle pdb=" C3' DA J 81 " pdb=" C2' DA J 81 " pdb=" C1' DA J 81 " ideal model delta sigma weight residual 101.60 104.83 -3.23 1.50e+00 4.44e-01 4.63e+00 angle pdb=" C3' DA J 111 " pdb=" C2' DA J 111 " pdb=" C1' DA J 111 " ideal model delta sigma weight residual 101.60 104.79 -3.19 1.50e+00 4.44e-01 4.53e+00 ... (remaining 24142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.38: 7367 14.38 - 28.77: 660 28.77 - 43.15: 752 43.15 - 57.54: 531 57.54 - 71.92: 48 Dihedral angle restraints: 9358 sinusoidal: 4865 harmonic: 4493 Sorted by residual: dihedral pdb=" N LYS C 76 " pdb=" CA LYS C 76 " pdb=" CB LYS C 76 " pdb=" CG LYS C 76 " ideal model delta sinusoidal sigma weight residual -60.00 -113.93 53.93 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CB ARG A 84 " pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 133.72 46.28 3 1.50e+01 4.44e-03 8.31e+00 dihedral pdb=" N ARG A 135 " pdb=" CA ARG A 135 " pdb=" CB ARG A 135 " pdb=" CG ARG A 135 " ideal model delta sinusoidal sigma weight residual -180.00 -135.41 -44.59 3 1.50e+01 4.44e-03 8.02e+00 ... (remaining 9355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1640 0.031 - 0.061: 645 0.061 - 0.092: 396 0.092 - 0.123: 116 0.123 - 0.154: 40 Chirality restraints: 2837 Sorted by residual: chirality pdb=" CA ILE L 255 " pdb=" N ILE L 255 " pdb=" C ILE L 255 " pdb=" CB ILE L 255 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA VAL L 97 " pdb=" N VAL L 97 " pdb=" C VAL L 97 " pdb=" CB VAL L 97 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA LYS A 116 " pdb=" N LYS A 116 " pdb=" C LYS A 116 " pdb=" CB LYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 2834 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 189 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO L 190 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO L 190 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 190 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 189 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.86e-01 pdb=" N PRO N 190 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO N 190 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO N 190 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 189 " -0.016 5.00e-02 4.00e+02 2.48e-02 9.86e-01 pdb=" N PRO M 190 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO M 190 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO M 190 " -0.014 5.00e-02 4.00e+02 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1582 2.74 - 3.28: 14128 3.28 - 3.82: 27630 3.82 - 4.36: 33462 4.36 - 4.90: 49245 Nonbonded interactions: 126047 Sorted by model distance: nonbonded pdb=" N4 DC I 18 " pdb=" O4 DT J 129 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR D 91 " pdb=" OE1 GLU D 94 " model vdw 2.339 3.040 nonbonded pdb=" N6 DA I 60 " pdb=" O6 DG J 87 " model vdw 2.344 3.120 nonbonded pdb=" N GLU H 94 " pdb=" OE1 GLU H 94 " model vdw 2.344 3.120 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.352 3.040 ... (remaining 126042 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 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.003 0.036 16820 Z= 0.137 Angle : 0.553 4.534 24147 Z= 0.345 Chirality : 0.046 0.154 2837 Planarity : 0.003 0.027 2185 Dihedral : 21.338 71.920 6444 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 0.14 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.18), residues: 1537 helix: -1.57 (0.17), residues: 636 sheet: -1.94 (0.26), residues: 320 loop : -1.84 (0.22), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 68 TYR 0.003 0.001 TYR B 99 PHE 0.002 0.000 PHE C 26 TRP 0.000 0.000 TRP K 146 HIS 0.001 0.000 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00267 (16820) covalent geometry : angle 0.55281 (24147) hydrogen bonds : bond 0.22812 ( 936) hydrogen bonds : angle 7.64638 ( 2360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7837 (tpt90) REVERT: B 51 ILE cc_start: 0.8981 (mm) cc_final: 0.8678 (mm) REVERT: C 65 GLU cc_start: 0.7811 (tt0) cc_final: 0.7595 (tt0) REVERT: C 69 ASN cc_start: 0.8206 (m-40) cc_final: 0.8003 (m-40) REVERT: C 73 ASP cc_start: 0.8965 (m-30) cc_final: 0.8700 (m-30) REVERT: C 93 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7693 (mm-30) REVERT: D 58 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8638 (mttt) REVERT: D 63 MET cc_start: 0.8635 (mmm) cc_final: 0.8405 (mmm) REVERT: D 72 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7252 (mm-30) REVERT: E 43 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7411 (mtp85) REVERT: E 61 LEU cc_start: 0.8738 (mt) cc_final: 0.8468 (mt) REVERT: E 78 ASP cc_start: 0.8246 (m-30) cc_final: 0.7906 (t0) REVERT: E 94 GLN cc_start: 0.8599 (mt0) cc_final: 0.7920 (mt0) REVERT: F 54 GLU cc_start: 0.8204 (tp30) cc_final: 0.7970 (tp30) REVERT: F 86 ASP cc_start: 0.8522 (m-30) cc_final: 0.8304 (m-30) REVERT: G 51 TYR cc_start: 0.9040 (t80) cc_final: 0.8785 (t80) REVERT: G 74 ASN cc_start: 0.8711 (m-40) cc_final: 0.8325 (m-40) REVERT: G 91 ASP cc_start: 0.8697 (t0) cc_final: 0.8455 (t70) REVERT: G 96 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8139 (mttt) REVERT: H 68 ASN cc_start: 0.8970 (m-40) cc_final: 0.8683 (m110) REVERT: M 142 PRO cc_start: 0.6318 (Cg_exo) cc_final: 0.5966 (Cg_endo) outliers start: 3 outliers final: 1 residues processed: 268 average time/residue: 0.1831 time to fit residues: 65.4019 Evaluate side-chains 204 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 28 GLN D 96 GLN D 110 HIS H 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.074455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063848 restraints weight = 75909.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065425 restraints weight = 35720.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.066418 restraints weight = 21677.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.067034 restraints weight = 15444.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067457 restraints weight = 12442.164| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16820 Z= 0.241 Angle : 0.622 5.927 24147 Z= 0.362 Chirality : 0.041 0.165 2837 Planarity : 0.005 0.044 2185 Dihedral : 27.040 76.212 4757 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.60 % Allowed : 6.49 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.21), residues: 1537 helix: 1.21 (0.20), residues: 618 sheet: -1.54 (0.27), residues: 328 loop : -0.89 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 100 TYR 0.018 0.002 TYR B 89 PHE 0.018 0.002 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00525 (16820) covalent geometry : angle 0.62165 (24147) hydrogen bonds : bond 0.05323 ( 936) hydrogen bonds : angle 4.19197 ( 2360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8304 (mmp) cc_final: 0.7928 (mmt) REVERT: A 130 ARG cc_start: 0.8318 (tpt90) cc_final: 0.7968 (tpt90) REVERT: C 73 ASP cc_start: 0.8653 (m-30) cc_final: 0.8238 (m-30) REVERT: D 48 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7607 (mp10) REVERT: D 63 MET cc_start: 0.8700 (mmm) cc_final: 0.8496 (mmm) REVERT: D 69 ASP cc_start: 0.8140 (t0) cc_final: 0.7766 (t0) REVERT: D 87 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8136 (mtp85) REVERT: D 90 ILE cc_start: 0.8818 (mm) cc_final: 0.8464 (mt) REVERT: D 121 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8602 (tttm) REVERT: E 43 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.7595 (mtp85) REVERT: E 63 ILE cc_start: 0.9013 (mt) cc_final: 0.8663 (mt) REVERT: E 78 ASP cc_start: 0.8455 (m-30) cc_final: 0.8214 (t0) REVERT: E 82 ASP cc_start: 0.8376 (t0) cc_final: 0.8129 (t0) REVERT: E 124 ASP cc_start: 0.8728 (m-30) cc_final: 0.8455 (m-30) REVERT: F 31 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8217 (p) REVERT: G 74 ASN cc_start: 0.8804 (m-40) cc_final: 0.8523 (m-40) REVERT: H 64 ASN cc_start: 0.8562 (m-40) cc_final: 0.7765 (m-40) REVERT: H 68 ASN cc_start: 0.9041 (m-40) cc_final: 0.8742 (m-40) REVERT: H 69 ASP cc_start: 0.8526 (t0) cc_final: 0.8277 (t0) outliers start: 18 outliers final: 11 residues processed: 230 average time/residue: 0.1626 time to fit residues: 51.0831 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 26 optimal weight: 0.0670 chunk 23 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 0.0170 chunk 69 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN C 85 GLN H 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.075323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064879 restraints weight = 75823.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066464 restraints weight = 35423.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.067480 restraints weight = 21289.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068095 restraints weight = 15224.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068527 restraints weight = 12236.414| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16820 Z= 0.147 Angle : 0.505 6.105 24147 Z= 0.298 Chirality : 0.036 0.151 2837 Planarity : 0.004 0.041 2185 Dihedral : 26.166 73.443 4757 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.73 % Allowed : 9.67 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.21), residues: 1537 helix: 2.11 (0.21), residues: 620 sheet: -0.96 (0.29), residues: 322 loop : -0.42 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 87 TYR 0.031 0.001 TYR B 89 PHE 0.011 0.001 PHE H 66 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00310 (16820) covalent geometry : angle 0.50497 (24147) hydrogen bonds : bond 0.03923 ( 936) hydrogen bonds : angle 3.47089 ( 2360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8223 (tpt90) cc_final: 0.7986 (tpt90) REVERT: C 42 GLU cc_start: 0.8036 (tp30) cc_final: 0.7782 (tp30) REVERT: C 85 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8457 (tp-100) REVERT: D 32 ARG cc_start: 0.6636 (mmt180) cc_final: 0.6414 (mtt90) REVERT: D 48 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7789 (mp10) REVERT: D 63 MET cc_start: 0.8626 (mmm) cc_final: 0.8332 (mmm) REVERT: D 69 ASP cc_start: 0.8061 (t0) cc_final: 0.7708 (t0) REVERT: D 121 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8644 (tttm) REVERT: E 124 ASP cc_start: 0.8707 (m-30) cc_final: 0.8498 (m-30) REVERT: F 31 THR cc_start: 0.8409 (p) cc_final: 0.8144 (p) REVERT: F 85 MET cc_start: 0.8177 (mmm) cc_final: 0.7915 (mmt) REVERT: G 73 ASP cc_start: 0.8319 (m-30) cc_final: 0.7960 (m-30) REVERT: G 74 ASN cc_start: 0.8802 (m-40) cc_final: 0.8517 (m-40) REVERT: G 93 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7724 (mm-30) REVERT: H 68 ASN cc_start: 0.9028 (m-40) cc_final: 0.8682 (m110) REVERT: H 69 ASP cc_start: 0.8520 (t0) cc_final: 0.8155 (t0) REVERT: H 77 GLU cc_start: 0.8031 (tp30) cc_final: 0.7636 (tp30) REVERT: H 106 GLU cc_start: 0.7871 (tp30) cc_final: 0.7620 (mm-30) outliers start: 12 outliers final: 8 residues processed: 219 average time/residue: 0.1587 time to fit residues: 47.7265 Evaluate side-chains 212 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN C 85 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.057007 restraints weight = 76776.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058475 restraints weight = 36329.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.059404 restraints weight = 22105.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059993 restraints weight = 15891.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060287 restraints weight = 12779.988| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16820 Z= 0.316 Angle : 0.677 8.403 24147 Z= 0.393 Chirality : 0.045 0.172 2837 Planarity : 0.006 0.054 2185 Dihedral : 27.405 88.461 4753 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.74 % Allowed : 12.70 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.21), residues: 1537 helix: 1.73 (0.20), residues: 633 sheet: -1.13 (0.29), residues: 308 loop : -0.64 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 82 TYR 0.027 0.002 TYR D 84 PHE 0.015 0.002 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00692 (16820) covalent geometry : angle 0.67740 (24147) hydrogen bonds : bond 0.06315 ( 936) hydrogen bonds : angle 4.56032 ( 2360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 THR cc_start: 0.9017 (m) cc_final: 0.8786 (p) REVERT: D 48 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7952 (mp10) REVERT: D 63 MET cc_start: 0.8855 (mmm) cc_final: 0.8631 (mmm) REVERT: D 69 ASP cc_start: 0.8211 (t0) cc_final: 0.7737 (t0) REVERT: D 121 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8393 (tttm) REVERT: F 85 MET cc_start: 0.8222 (mmm) cc_final: 0.7983 (mmt) REVERT: F 96 ARG cc_start: 0.8921 (ptp-110) cc_final: 0.8698 (ptp-110) REVERT: G 91 ASP cc_start: 0.8645 (t0) cc_final: 0.8291 (t0) REVERT: G 93 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7958 (mm-30) REVERT: H 68 ASN cc_start: 0.9046 (m-40) cc_final: 0.8669 (m-40) REVERT: H 69 ASP cc_start: 0.8607 (t0) cc_final: 0.8383 (t0) REVERT: H 77 GLU cc_start: 0.8110 (tp30) cc_final: 0.7833 (tp30) REVERT: H 81 LEU cc_start: 0.9162 (mt) cc_final: 0.8827 (mt) outliers start: 19 outliers final: 10 residues processed: 218 average time/residue: 0.1630 time to fit residues: 48.5486 Evaluate side-chains 212 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 chunk 126 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN ** C 105 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 = 0.3522 r_free = 0.3522 target = 0.068818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059583 restraints weight = 75797.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061028 restraints weight = 35761.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061948 restraints weight = 21809.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062523 restraints weight = 15756.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062871 restraints weight = 12720.177| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16820 Z= 0.164 Angle : 0.537 7.219 24147 Z= 0.314 Chirality : 0.037 0.142 2837 Planarity : 0.004 0.045 2185 Dihedral : 26.538 72.287 4753 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.88 % Allowed : 13.42 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.22), residues: 1537 helix: 2.16 (0.21), residues: 632 sheet: -0.70 (0.30), residues: 304 loop : -0.20 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.042 0.002 TYR D 84 PHE 0.007 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS H 110 Details of bonding type rmsd covalent geometry : bond 0.00352 (16820) covalent geometry : angle 0.53717 (24147) hydrogen bonds : bond 0.03831 ( 936) hydrogen bonds : angle 3.52096 ( 2360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 SER cc_start: 0.8701 (m) cc_final: 0.8260 (m) REVERT: D 48 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7888 (mp10) REVERT: D 63 MET cc_start: 0.8764 (mmm) cc_final: 0.8477 (mmm) REVERT: D 69 ASP cc_start: 0.8116 (t0) cc_final: 0.7858 (t0) REVERT: D 121 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8587 (tttm) REVERT: E 51 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7653 (mm-30) REVERT: F 85 MET cc_start: 0.8125 (mmm) cc_final: 0.7902 (mmt) REVERT: H 68 ASN cc_start: 0.8991 (m-40) cc_final: 0.8620 (m110) REVERT: H 69 ASP cc_start: 0.8497 (t0) cc_final: 0.8203 (t0) REVERT: H 77 GLU cc_start: 0.7943 (tp30) cc_final: 0.7621 (tp30) REVERT: H 106 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7294 (mm-30) outliers start: 13 outliers final: 9 residues processed: 217 average time/residue: 0.1678 time to fit residues: 49.7256 Evaluate side-chains 214 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 0.9990 chunk 133 optimal weight: 0.0070 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 26 ASN B 28 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN G 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.068788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059628 restraints weight = 75434.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061074 restraints weight = 35680.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061986 restraints weight = 21734.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062563 restraints weight = 15725.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.062886 restraints weight = 12669.037| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16820 Z= 0.160 Angle : 0.521 6.565 24147 Z= 0.307 Chirality : 0.036 0.149 2837 Planarity : 0.004 0.043 2185 Dihedral : 26.307 73.257 4753 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.88 % Allowed : 13.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1537 helix: 2.33 (0.21), residues: 636 sheet: -0.57 (0.30), residues: 316 loop : -0.11 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 87 TYR 0.046 0.002 TYR D 84 PHE 0.006 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00346 (16820) covalent geometry : angle 0.52099 (24147) hydrogen bonds : bond 0.03712 ( 936) hydrogen bonds : angle 3.35503 ( 2360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 LYS cc_start: 0.9127 (ttpt) cc_final: 0.8776 (ttpp) REVERT: C 41 SER cc_start: 0.8682 (m) cc_final: 0.8235 (m) REVERT: D 48 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7848 (mp10) REVERT: D 63 MET cc_start: 0.8708 (mmm) cc_final: 0.8434 (mmm) REVERT: D 69 ASP cc_start: 0.8134 (t0) cc_final: 0.7866 (t0) REVERT: D 121 LYS cc_start: 0.8809 (ttpt) cc_final: 0.8567 (tttm) REVERT: E 51 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 89 TYR cc_start: 0.8664 (m-10) cc_final: 0.8423 (m-10) REVERT: H 68 ASN cc_start: 0.8972 (m-40) cc_final: 0.8602 (m110) REVERT: H 69 ASP cc_start: 0.8433 (t0) cc_final: 0.8196 (t0) REVERT: H 77 GLU cc_start: 0.8082 (tp30) cc_final: 0.7779 (tp30) REVERT: H 84 TYR cc_start: 0.8259 (m-10) cc_final: 0.7919 (m-80) REVERT: H 106 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7259 (mm-30) outliers start: 13 outliers final: 10 residues processed: 211 average time/residue: 0.1527 time to fit residues: 44.0549 Evaluate side-chains 213 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 28 GLN E 126 GLN G 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.055966 restraints weight = 76398.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.057360 restraints weight = 36349.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058229 restraints weight = 22244.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058795 restraints weight = 16129.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059155 restraints weight = 13017.510| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16820 Z= 0.280 Angle : 0.619 7.551 24147 Z= 0.358 Chirality : 0.041 0.159 2837 Planarity : 0.005 0.042 2185 Dihedral : 26.871 81.542 4753 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 13.42 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.22), residues: 1537 helix: 2.11 (0.21), residues: 634 sheet: -0.82 (0.29), residues: 320 loop : -0.15 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 32 TYR 0.072 0.002 TYR D 84 PHE 0.013 0.001 PHE E 85 TRP 0.000 0.000 TRP K 146 HIS 0.007 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00620 (16820) covalent geometry : angle 0.61892 (24147) hydrogen bonds : bond 0.05029 ( 936) hydrogen bonds : angle 3.87038 ( 2360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 41 SER cc_start: 0.8771 (m) cc_final: 0.8320 (m) REVERT: D 48 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7939 (mp10) REVERT: D 63 MET cc_start: 0.8829 (mmm) cc_final: 0.8602 (mmm) REVERT: D 69 ASP cc_start: 0.8163 (t0) cc_final: 0.7887 (t0) REVERT: D 121 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8508 (tttm) REVERT: E 51 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7632 (mm-30) REVERT: G 75 LYS cc_start: 0.7433 (tptt) cc_final: 0.7210 (tptt) REVERT: H 68 ASN cc_start: 0.9014 (m-40) cc_final: 0.8633 (m110) REVERT: H 69 ASP cc_start: 0.8581 (t0) cc_final: 0.8380 (t0) REVERT: H 84 TYR cc_start: 0.8307 (m-10) cc_final: 0.8024 (m-80) REVERT: H 106 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7078 (mm-30) REVERT: H 109 LYS cc_start: 0.8697 (ptpp) cc_final: 0.7966 (ptpp) outliers start: 16 outliers final: 13 residues processed: 213 average time/residue: 0.1552 time to fit residues: 45.3607 Evaluate side-chains 219 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 26 ASN B 28 GLN G 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057236 restraints weight = 76074.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058617 restraints weight = 35634.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059497 restraints weight = 21732.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060053 restraints weight = 15667.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060360 restraints weight = 12637.239| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16820 Z= 0.183 Angle : 0.554 10.025 24147 Z= 0.322 Chirality : 0.037 0.144 2837 Planarity : 0.004 0.043 2185 Dihedral : 26.563 73.713 4753 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.45 % Allowed : 13.85 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.22), residues: 1537 helix: 2.27 (0.21), residues: 622 sheet: -0.58 (0.30), residues: 318 loop : -0.02 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 36 TYR 0.070 0.002 TYR D 84 PHE 0.007 0.001 PHE F 62 TRP 0.000 0.000 TRP K 146 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00401 (16820) covalent geometry : angle 0.55360 (24147) hydrogen bonds : bond 0.03904 ( 936) hydrogen bonds : angle 3.48031 ( 2360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 16 LYS cc_start: 0.9149 (ttpt) cc_final: 0.8799 (ttpp) REVERT: C 41 SER cc_start: 0.8726 (m) cc_final: 0.8277 (m) REVERT: D 48 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7916 (mp10) REVERT: D 58 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8202 (mtmm) REVERT: D 63 MET cc_start: 0.8788 (mmm) cc_final: 0.8548 (mmm) REVERT: D 69 ASP cc_start: 0.8149 (t0) cc_final: 0.7894 (t0) REVERT: D 121 LYS cc_start: 0.8834 (ttpt) cc_final: 0.8551 (tttm) REVERT: E 51 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7594 (mm-30) REVERT: F 89 TYR cc_start: 0.8880 (m-10) cc_final: 0.8319 (m-10) REVERT: H 68 ASN cc_start: 0.9000 (m-40) cc_final: 0.8620 (m110) REVERT: H 69 ASP cc_start: 0.8480 (t0) cc_final: 0.8276 (t0) REVERT: H 84 TYR cc_start: 0.8255 (m-10) cc_final: 0.7924 (m-10) REVERT: H 106 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7306 (mm-30) REVERT: H 109 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8134 (ptpp) outliers start: 17 outliers final: 12 residues processed: 215 average time/residue: 0.1610 time to fit residues: 47.4332 Evaluate side-chains 220 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 10.0000 chunk 167 optimal weight: 0.3980 chunk 170 optimal weight: 0.0570 chunk 144 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 148 optimal weight: 0.5980 chunk 161 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 26 ASN B 28 GLN E 126 GLN G 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.066976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058022 restraints weight = 76108.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059458 restraints weight = 35156.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060370 restraints weight = 21135.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060965 restraints weight = 15091.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061341 restraints weight = 12071.146| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16820 Z= 0.152 Angle : 0.530 6.225 24147 Z= 0.312 Chirality : 0.036 0.146 2837 Planarity : 0.004 0.044 2185 Dihedral : 26.379 73.029 4753 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.88 % Allowed : 14.00 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.22), residues: 1537 helix: 2.35 (0.21), residues: 622 sheet: -0.27 (0.31), residues: 306 loop : 0.01 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.053 0.002 TYR D 84 PHE 0.008 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00329 (16820) covalent geometry : angle 0.52966 (24147) hydrogen bonds : bond 0.03466 ( 936) hydrogen bonds : angle 3.30148 ( 2360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 26 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8425 (t0) REVERT: C 16 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8880 (ttmm) REVERT: C 41 SER cc_start: 0.8674 (m) cc_final: 0.8205 (m) REVERT: C 42 GLU cc_start: 0.8043 (tp30) cc_final: 0.7798 (tm-30) REVERT: C 96 LYS cc_start: 0.8964 (ttpt) cc_final: 0.8763 (tppt) REVERT: D 48 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7862 (mp10) REVERT: D 63 MET cc_start: 0.8745 (mmm) cc_final: 0.8432 (mmm) REVERT: D 69 ASP cc_start: 0.8105 (t0) cc_final: 0.7848 (t0) REVERT: D 121 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8552 (tttm) REVERT: E 51 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7629 (mm-30) REVERT: F 89 TYR cc_start: 0.8835 (m-10) cc_final: 0.8270 (m-10) REVERT: H 68 ASN cc_start: 0.9041 (m-40) cc_final: 0.8594 (m110) REVERT: H 69 ASP cc_start: 0.8517 (t0) cc_final: 0.8282 (t0) REVERT: H 84 TYR cc_start: 0.8155 (m-10) cc_final: 0.7873 (m-10) REVERT: H 106 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7147 (mm-30) REVERT: H 109 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8074 (ptpp) outliers start: 13 outliers final: 10 residues processed: 212 average time/residue: 0.1564 time to fit residues: 45.4860 Evaluate side-chains 217 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 70 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 173 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 28 GLN E 126 GLN G 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058448 restraints weight = 75980.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059885 restraints weight = 35156.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060787 restraints weight = 21091.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061325 restraints weight = 15064.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.061721 restraints weight = 12143.680| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16820 Z= 0.151 Angle : 0.546 9.568 24147 Z= 0.316 Chirality : 0.036 0.148 2837 Planarity : 0.004 0.044 2185 Dihedral : 26.297 74.749 4753 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 14.72 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.22), residues: 1537 helix: 2.32 (0.21), residues: 626 sheet: -0.19 (0.32), residues: 294 loop : 0.18 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.063 0.002 TYR D 84 PHE 0.008 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00326 (16820) covalent geometry : angle 0.54558 (24147) hydrogen bonds : bond 0.03452 ( 936) hydrogen bonds : angle 3.26043 ( 2360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8376 (t0) REVERT: C 16 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8834 (ttmm) REVERT: C 41 SER cc_start: 0.8680 (m) cc_final: 0.8168 (m) REVERT: C 42 GLU cc_start: 0.8021 (tp30) cc_final: 0.7773 (tm-30) REVERT: D 48 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7875 (mp10) REVERT: D 63 MET cc_start: 0.8713 (mmm) cc_final: 0.8432 (mmm) REVERT: D 69 ASP cc_start: 0.8090 (t0) cc_final: 0.7837 (t0) REVERT: D 121 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8556 (tttm) REVERT: E 51 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7628 (mm-30) REVERT: F 89 TYR cc_start: 0.8682 (m-10) cc_final: 0.8310 (m-10) REVERT: H 68 ASN cc_start: 0.9027 (m-40) cc_final: 0.8585 (m110) REVERT: H 69 ASP cc_start: 0.8511 (t0) cc_final: 0.8272 (t0) REVERT: H 84 TYR cc_start: 0.8253 (m-10) cc_final: 0.7892 (m-10) REVERT: H 106 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7166 (mm-30) REVERT: H 109 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8141 (ptpp) outliers start: 12 outliers final: 10 residues processed: 213 average time/residue: 0.1565 time to fit residues: 46.1246 Evaluate side-chains 217 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 29 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 130 optimal weight: 0.0070 chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 112 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN B 28 GLN B 94 GLN D 85 ASN F 28 GLN G 69 ASN H 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.067274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058495 restraints weight = 75510.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059887 restraints weight = 35834.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060766 restraints weight = 21786.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061332 restraints weight = 15687.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061638 restraints weight = 12650.944| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16820 Z= 0.155 Angle : 0.552 11.077 24147 Z= 0.319 Chirality : 0.036 0.162 2837 Planarity : 0.004 0.043 2185 Dihedral : 26.269 75.549 4753 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 14.14 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1537 helix: 2.39 (0.21), residues: 624 sheet: -0.15 (0.31), residues: 310 loop : 0.18 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 36 TYR 0.040 0.002 TYR B 89 PHE 0.007 0.001 PHE D 71 TRP 0.000 0.000 TRP K 146 HIS 0.005 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00337 (16820) covalent geometry : angle 0.55156 (24147) hydrogen bonds : bond 0.03479 ( 936) hydrogen bonds : angle 3.23803 ( 2360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.60 seconds wall clock time: 52 minutes 29.70 seconds (3149.70 seconds total)