Starting phenix.real_space_refine on Sat Dec 28 02:38:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.map" model { file = "/net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a93_15267/12_2024/8a93_15267.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 2 5.21 5 S 7 5.16 5 C 4491 2.51 5 N 1388 2.21 5 O 1417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7353 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2692 Chain: "B" Number of atoms: 2643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2673 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 81 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 323 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 685 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "X" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.66, per 1000 atoms: 1.04 Number of scatterers: 7353 At special positions: 0 Unit cell: (82.56, 99.76, 111.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 7 16.00 P 48 15.00 Mg 2 11.99 O 1417 8.00 N 1388 7.00 C 4491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 51.7% alpha, 14.6% beta 11 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.173A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.680A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 removed outlier: 3.976A pdb=" N ALA A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 202 removed outlier: 3.896A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.512A pdb=" N ASP A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.541A pdb=" N LEU B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.876A pdb=" N LEU B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 141 through 163 removed outlier: 3.947A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 205 removed outlier: 4.061A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.530A pdb=" N ASP B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'C' and resid 38 through 49 removed outlier: 3.636A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 removed outlier: 4.170A pdb=" N LEU D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.656A pdb=" N GLN D 26 " --> pdb=" O PRO D 22 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.713A pdb=" N ALA D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 3.772A pdb=" N SER F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 5.337A pdb=" N LEU A 3 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 73 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.600A pdb=" N LEU A 319 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N CYS A 331 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 27 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 333 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 29 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.400A pdb=" N VAL A 92 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.613A pdb=" N ASP A 246 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.137A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 93 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.186A pdb=" N VAL B 111 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP B 293 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 113 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 290 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY B 24 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 319 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B 26 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY B 321 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU B 28 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N CYS B 331 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 27 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 333 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 29 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.533A pdb=" N ASP B 246 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 101 through 104 removed outlier: 6.135A pdb=" N ALA F 81 " --> pdb=" O HIS F 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 80 " --> pdb=" O VAL F 136 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2126 1.33 - 1.45: 1259 1.45 - 1.57: 4084 1.57 - 1.69: 94 1.69 - 1.81: 10 Bond restraints: 7573 Sorted by residual: bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.593 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 7568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 10317 2.20 - 4.40: 107 4.40 - 6.60: 15 6.60 - 8.80: 5 8.80 - 11.01: 2 Bond angle restraints: 10446 Sorted by residual: angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O3A ANP A 901 " ideal model delta sigma weight residual 103.40 114.41 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O3A ANP B 901 " ideal model delta sigma weight residual 103.40 114.37 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" PA ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 125.41 133.35 -7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" PA ANP B 901 " pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 125.41 133.13 -7.72 3.00e+00 1.11e-01 6.61e+00 angle pdb=" CB LYS F 118 " pdb=" CG LYS F 118 " pdb=" CD LYS F 118 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.53e+00 ... (remaining 10441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3752 17.95 - 35.89: 460 35.89 - 53.84: 237 53.84 - 71.79: 29 71.79 - 89.73: 10 Dihedral angle restraints: 4488 sinusoidal: 2139 harmonic: 2349 Sorted by residual: dihedral pdb=" CG ARG B 191 " pdb=" CD ARG B 191 " pdb=" NE ARG B 191 " pdb=" CZ ARG B 191 " ideal model delta sinusoidal sigma weight residual 90.00 134.98 -44.98 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CB GLU A 17 " pdb=" CG GLU A 17 " pdb=" CD GLU A 17 " pdb=" OE1 GLU A 17 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA GLU B 294 " pdb=" C GLU B 294 " pdb=" N TRP B 295 " pdb=" CA TRP B 295 " ideal model delta harmonic sigma weight residual 180.00 -163.73 -16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1056 0.057 - 0.113: 112 0.113 - 0.170: 4 0.170 - 0.227: 0 0.227 - 0.283: 2 Chirality restraints: 1174 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL F 161 " pdb=" N VAL F 161 " pdb=" C VAL F 161 " pdb=" CB VAL F 161 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1171 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 114 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 115 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 123 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 124 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " 0.017 5.00e-02 4.00e+02 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 57 2.64 - 3.20: 5862 3.20 - 3.77: 10406 3.77 - 4.33: 13926 4.33 - 4.90: 22994 Nonbonded interactions: 53245 Sorted by model distance: nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.078 2.170 nonbonded pdb=" O1B ANP B 901 " pdb="MG MG B 902 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.145 2.170 ... (remaining 53240 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 1 through 51 or resid 53 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ gh 341 or resid 901 through 902)) selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 341 or resid 901 through 902)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.680 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.610 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.005 0.166 7573 Z= 0.247 Angle : 0.574 11.006 10446 Z= 0.271 Chirality : 0.036 0.283 1174 Planarity : 0.004 0.035 1203 Dihedral : 18.984 89.732 2982 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.64 % Allowed : 0.00 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.31), residues: 818 helix: 2.68 (0.28), residues: 355 sheet: 0.94 (0.42), residues: 148 loop : -1.14 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 PHE 0.008 0.001 PHE D 34 TYR 0.004 0.001 TYR B 178 ARG 0.008 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: D 16 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7720 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2916 time to fit residues: 31.3892 Evaluate side-chains 71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7573 Z= 0.255 Angle : 0.586 7.354 10446 Z= 0.305 Chirality : 0.039 0.146 1174 Planarity : 0.004 0.040 1203 Dihedral : 19.767 88.504 1458 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.12 % Allowed : 6.70 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 818 helix: 2.44 (0.27), residues: 369 sheet: 1.40 (0.43), residues: 146 loop : -1.38 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.007 0.001 HIS A 277 PHE 0.011 0.001 PHE A 193 TYR 0.008 0.001 TYR B 79 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.814 Fit side-chains REVERT: A 102 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7713 (mtm-85) REVERT: B 173 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7841 (mtt90) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.3198 time to fit residues: 31.2227 Evaluate side-chains 72 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7573 Z= 0.217 Angle : 0.527 6.633 10446 Z= 0.275 Chirality : 0.037 0.165 1174 Planarity : 0.004 0.046 1203 Dihedral : 19.416 89.543 1458 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.12 % Allowed : 8.61 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 818 helix: 2.50 (0.27), residues: 369 sheet: 1.65 (0.43), residues: 146 loop : -1.42 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 105 HIS 0.005 0.001 HIS A 277 PHE 0.010 0.001 PHE D 34 TYR 0.007 0.001 TYR B 79 ARG 0.004 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.861 Fit side-chains REVERT: A 97 LYS cc_start: 0.7953 (ptmm) cc_final: 0.7700 (ptpp) REVERT: A 102 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7647 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.3203 time to fit residues: 30.4528 Evaluate side-chains 71 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 8 optimal weight: 0.0270 chunk 37 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7573 Z= 0.161 Angle : 0.501 6.593 10446 Z= 0.258 Chirality : 0.036 0.127 1174 Planarity : 0.004 0.045 1203 Dihedral : 19.160 84.273 1458 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.96 % Allowed : 10.21 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 818 helix: 2.60 (0.27), residues: 370 sheet: 1.69 (0.43), residues: 148 loop : -1.28 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 105 HIS 0.003 0.001 HIS A 257 PHE 0.008 0.001 PHE D 34 TYR 0.006 0.001 TYR B 79 ARG 0.005 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.793 Fit side-chains REVERT: A 102 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7640 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 0.3107 time to fit residues: 31.0134 Evaluate side-chains 74 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7573 Z= 0.409 Angle : 0.632 6.618 10446 Z= 0.327 Chirality : 0.041 0.156 1174 Planarity : 0.005 0.046 1203 Dihedral : 19.323 88.463 1458 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.91 % Allowed : 11.00 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.30), residues: 818 helix: 2.38 (0.27), residues: 368 sheet: 1.71 (0.43), residues: 142 loop : -1.64 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.009 0.002 HIS A 277 PHE 0.017 0.002 PHE A 193 TYR 0.008 0.001 TYR F 151 ARG 0.005 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.780 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.3070 time to fit residues: 30.8487 Evaluate side-chains 76 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7573 Z= 0.206 Angle : 0.532 6.618 10446 Z= 0.276 Chirality : 0.037 0.157 1174 Planarity : 0.004 0.048 1203 Dihedral : 19.205 86.274 1458 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.44 % Allowed : 12.28 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 818 helix: 2.51 (0.27), residues: 370 sheet: 1.56 (0.43), residues: 148 loop : -1.43 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.005 0.001 HIS A 277 PHE 0.010 0.001 PHE D 34 TYR 0.006 0.001 TYR B 79 ARG 0.005 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.797 Fit side-chains REVERT: A 97 LYS cc_start: 0.7943 (ptmm) cc_final: 0.7528 (ttmt) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.3137 time to fit residues: 30.7233 Evaluate side-chains 77 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain F residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7573 Z= 0.242 Angle : 0.541 6.261 10446 Z= 0.281 Chirality : 0.037 0.156 1174 Planarity : 0.004 0.048 1203 Dihedral : 19.223 86.661 1458 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.39 % Allowed : 11.64 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.30), residues: 818 helix: 2.55 (0.27), residues: 369 sheet: 1.85 (0.43), residues: 141 loop : -1.53 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.006 0.001 HIS A 277 PHE 0.011 0.001 PHE A 193 TYR 0.012 0.001 TYR F 102 ARG 0.006 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.796 Fit side-chains REVERT: A 73 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: A 97 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7601 (ttmt) REVERT: A 102 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7590 (mtm-85) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.2982 time to fit residues: 30.7366 Evaluate side-chains 83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7573 Z= 0.171 Angle : 0.512 6.726 10446 Z= 0.264 Chirality : 0.035 0.159 1174 Planarity : 0.004 0.047 1203 Dihedral : 19.122 84.578 1458 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.07 % Allowed : 12.12 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.30), residues: 818 helix: 2.64 (0.27), residues: 370 sheet: 1.69 (0.42), residues: 148 loop : -1.29 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.004 0.001 HIS A 277 PHE 0.009 0.001 PHE D 34 TYR 0.006 0.001 TYR B 79 ARG 0.006 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.744 Fit side-chains REVERT: A 73 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7933 (tm-30) REVERT: A 97 LYS cc_start: 0.7856 (ptmm) cc_final: 0.7450 (ttmt) REVERT: A 102 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: D 16 ARG cc_start: 0.8116 (mtm110) cc_final: 0.7677 (ptm-80) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.2933 time to fit residues: 31.3148 Evaluate side-chains 82 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7573 Z= 0.212 Angle : 0.521 6.356 10446 Z= 0.270 Chirality : 0.036 0.156 1174 Planarity : 0.004 0.046 1203 Dihedral : 19.135 84.688 1458 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.07 % Allowed : 12.12 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 818 helix: 2.63 (0.27), residues: 370 sheet: 1.71 (0.42), residues: 148 loop : -1.32 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.005 0.001 HIS A 277 PHE 0.009 0.001 PHE A 193 TYR 0.012 0.001 TYR F 102 ARG 0.005 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.787 Fit side-chains REVERT: A 73 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 97 LYS cc_start: 0.7854 (ptmm) cc_final: 0.7462 (ttmt) REVERT: A 102 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: B 173 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7648 (mtm-85) REVERT: D 16 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7746 (ptm-80) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.3110 time to fit residues: 31.3632 Evaluate side-chains 83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 7573 Z= 0.369 Angle : 0.607 6.114 10446 Z= 0.315 Chirality : 0.039 0.154 1174 Planarity : 0.005 0.046 1203 Dihedral : 19.321 88.433 1458 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.23 % Allowed : 12.28 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 818 helix: 2.46 (0.27), residues: 369 sheet: 1.78 (0.42), residues: 141 loop : -1.63 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.009 0.002 HIS A 277 PHE 0.015 0.002 PHE A 193 TYR 0.008 0.001 TYR F 151 ARG 0.004 0.000 ARG D 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.911 Fit side-chains REVERT: A 73 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: A 97 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7514 (ttmt) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.3103 time to fit residues: 30.9042 Evaluate side-chains 79 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.1980 chunk 10 optimal weight: 0.0570 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075693 restraints weight = 30463.563| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 4.59 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7573 Z= 0.158 Angle : 0.524 9.935 10446 Z= 0.267 Chirality : 0.036 0.164 1174 Planarity : 0.004 0.046 1203 Dihedral : 19.135 84.582 1458 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.59 % Allowed : 12.92 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 818 helix: 2.66 (0.27), residues: 371 sheet: 1.55 (0.42), residues: 153 loop : -1.24 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.003 0.001 HIS A 257 PHE 0.008 0.001 PHE D 34 TYR 0.006 0.001 TYR B 79 ARG 0.006 0.000 ARG D 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1773.58 seconds wall clock time: 32 minutes 48.46 seconds (1968.46 seconds total)