Starting phenix.real_space_refine on Fri Feb 14 05:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.map" model { file = "/net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wfg_32465/02_2025/7wfg_32465.cif" } resolution = 4.33 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 Fe 12 7.16 5 S 64 5.16 5 C 6304 2.51 5 N 1677 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2812 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 335} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 86 Chain: "I" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1236 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "J" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1120 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 146} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 118 Chain: "K" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1199 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 154} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 646 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 70} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "M" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 767 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 110 Chain: "N" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 909 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 132} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 183 Chain: "O" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 2 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 603 Classifications: {'peptide': 122} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 115} Link IDs: {'TRANS': 121} Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 122} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3592 SG CYS I 110 39.258 36.676 84.998 1.00144.09 S ATOM 5818 SG CYS K 108 52.007 42.309 71.485 1.00166.07 S Time building chain proxies: 6.35, per 1000 atoms: 0.65 Number of scatterers: 9836 At special positions: 0 Unit cell: (113.36, 119.6, 121.68, 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) Fe 12 26.01 S 64 16.00 O 1779 8.00 N 1677 7.00 C 6304 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: 2.74 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 110 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 104 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 114 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 67 " pdb=" SF4 K 301 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 108 " Number of angles added : 18 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 41.5% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'H' and resid 50 through 58 removed outlier: 3.586A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 75 through 91 removed outlier: 3.691A pdb=" N GLU H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 125 Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 134 through 149 removed outlier: 4.614A pdb=" N PHE H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 191 removed outlier: 4.180A pdb=" N CYS H 179 " --> pdb=" O CYS H 175 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP H 180 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU H 185 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS H 191 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 Processing helix chain 'H' and resid 210 through 215 Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 232 through 237 Processing helix chain 'H' and resid 256 through 278 Processing helix chain 'H' and resid 356 through 362 removed outlier: 3.767A pdb=" N ILE H 360 " --> pdb=" O PRO H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 376 through 384 Processing helix chain 'I' and resid 7 through 33 Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.022A pdb=" N ARG I 144 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 152 removed outlier: 4.082A pdb=" N ASP I 152 " --> pdb=" O VAL I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 35 Processing helix chain 'J' and resid 36 through 45 Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 151 through 155 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 42 through 48 removed outlier: 3.824A pdb=" N ILE K 46 " --> pdb=" O CYS K 43 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU K 47 " --> pdb=" O CYS K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 95 Processing helix chain 'K' and resid 112 through 116 removed outlier: 3.653A pdb=" N PHE K 115 " --> pdb=" O GLY K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 129 removed outlier: 3.990A pdb=" N LYS K 128 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 Processing helix chain 'K' and resid 161 through 166 removed outlier: 3.724A pdb=" N ASP K 164 " --> pdb=" O ILE K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 107 Processing helix chain 'L' and resid 107 through 119 removed outlier: 4.213A pdb=" N ILE L 111 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 138 Processing helix chain 'L' and resid 139 through 144 removed outlier: 3.849A pdb=" N LEU L 143 " --> pdb=" O PRO L 140 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU L 144 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 150 Processing helix chain 'M' and resid 156 through 177 Processing helix chain 'N' and resid 63 through 72 Processing helix chain 'N' and resid 86 through 95 removed outlier: 4.146A pdb=" N LEU N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 116 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 166 through 179 Proline residue: N 176 - end of helix Processing helix chain 'T' and resid 2 through 6 removed outlier: 4.304A pdb=" N UNK T 6 " --> pdb=" O UNK T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 18 Processing helix chain 'T' and resid 25 through 39 removed outlier: 3.675A pdb=" N UNK T 39 " --> pdb=" O UNK T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 62 Processing helix chain 'T' and resid 62 through 73 Processing helix chain 'T' and resid 98 through 121 removed outlier: 3.683A pdb=" N UNK T 102 " --> pdb=" O UNK T 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 27 through 30 removed outlier: 3.521A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE H 29 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 36 through 37 removed outlier: 3.956A pdb=" N MET H 372 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 325 through 330 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AA5, first strand: chain 'I' and resid 80 through 82 removed outlier: 6.796A pdb=" N VAL I 80 " --> pdb=" O TYR I 97 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR I 97 " --> pdb=" O VAL I 80 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP I 82 " --> pdb=" O LEU I 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 17 through 21 removed outlier: 5.953A pdb=" N THR J 28 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU J 27 " --> pdb=" O CYS J 85 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS J 87 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU J 29 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE J 89 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE J 31 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N HIS J 91 " --> pdb=" O ILE J 31 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 96 through 98 removed outlier: 3.849A pdb=" N ASP J 123 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 102 through 104 removed outlier: 8.505A pdb=" N VAL K 102 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR K 135 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA K 104 " --> pdb=" O TYR K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'N' and resid 99 through 103 removed outlier: 6.687A pdb=" N TYR N 99 " --> pdb=" O VAL N 156 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL N 158 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU N 101 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 80 through 81 removed outlier: 3.827A pdb=" N GLY O 114 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU O 129 " --> pdb=" O LEU O 117 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU O 119 " --> pdb=" O TYR O 127 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR O 127 " --> pdb=" O LEU O 119 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 3.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 3991 1.42 - 1.64: 5927 1.64 - 1.86: 82 1.86 - 2.09: 0 2.09 - 2.31: 36 Bond restraints: 10036 Sorted by residual: bond pdb=" C ARG L 152 " pdb=" N LYS L 153 " ideal model delta sigma weight residual 1.332 1.201 0.132 1.40e-02 5.10e+03 8.86e+01 bond pdb=" C GLU I 68 " pdb=" N VAL I 69 " ideal model delta sigma weight residual 1.334 1.265 0.068 1.28e-02 6.10e+03 2.86e+01 bond pdb=" C PRO N 148 " pdb=" N PRO N 149 " ideal model delta sigma weight residual 1.326 1.392 -0.065 1.44e-02 4.82e+03 2.07e+01 bond pdb=" N ARG N 179 " pdb=" CA ARG N 179 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.62e+01 bond pdb=" N LEU N 175 " pdb=" CA LEU N 175 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12868 1.95 - 3.90: 634 3.90 - 5.85: 102 5.85 - 7.80: 29 7.80 - 9.75: 11 Bond angle restraints: 13644 Sorted by residual: angle pdb=" N PRO K 140 " pdb=" CA PRO K 140 " pdb=" C PRO K 140 " ideal model delta sigma weight residual 110.70 120.21 -9.51 1.22e+00 6.72e-01 6.08e+01 angle pdb=" N SER N 177 " pdb=" CA SER N 177 " pdb=" C SER N 177 " ideal model delta sigma weight residual 113.23 104.14 9.09 1.24e+00 6.50e-01 5.37e+01 angle pdb=" N LEU K 37 " pdb=" CA LEU K 37 " pdb=" C LEU K 37 " ideal model delta sigma weight residual 113.02 106.16 6.86 1.20e+00 6.94e-01 3.27e+01 angle pdb=" N PRO L 109 " pdb=" CA PRO L 109 " pdb=" C PRO L 109 " ideal model delta sigma weight residual 110.70 117.06 -6.36 1.22e+00 6.72e-01 2.72e+01 angle pdb=" N ASN N 181 " pdb=" CA ASN N 181 " pdb=" C ASN N 181 " ideal model delta sigma weight residual 114.39 107.58 6.81 1.45e+00 4.76e-01 2.21e+01 ... (remaining 13639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 5624 14.90 - 29.80: 312 29.80 - 44.70: 96 44.70 - 59.60: 26 59.60 - 74.51: 2 Dihedral angle restraints: 6060 sinusoidal: 2097 harmonic: 3963 Sorted by residual: dihedral pdb=" CA THR K 117 " pdb=" C THR K 117 " pdb=" N ASP K 118 " pdb=" CA ASP K 118 " ideal model delta harmonic sigma weight residual -180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA GLY H 218 " pdb=" C GLY H 218 " pdb=" N LEU H 219 " pdb=" CA LEU H 219 " ideal model delta harmonic sigma weight residual 180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ARG L 152 " pdb=" C ARG L 152 " pdb=" N LYS L 153 " pdb=" CA LYS L 153 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1231 0.070 - 0.139: 265 0.139 - 0.209: 52 0.209 - 0.278: 14 0.278 - 0.348: 1 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA LEU H 32 " pdb=" N LEU H 32 " pdb=" C LEU H 32 " pdb=" CB LEU H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA ARG M 161 " pdb=" N ARG M 161 " pdb=" C ARG M 161 " pdb=" CB ARG M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE I 65 " pdb=" CA ILE I 65 " pdb=" CG1 ILE I 65 " pdb=" CG2 ILE I 65 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1560 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU K 136 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO K 137 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO K 137 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 137 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 64 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO H 65 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP J 140 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO J 141 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 141 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 141 " 0.033 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 834 2.74 - 3.28: 9622 3.28 - 3.82: 16282 3.82 - 4.36: 18343 4.36 - 4.90: 30572 Nonbonded interactions: 75653 Sorted by model distance: nonbonded pdb=" OE2 GLU H 146 " pdb=" N SER I 50 " model vdw 2.204 3.120 nonbonded pdb=" CB ALA H 165 " pdb=" NH1 ARG I 52 " model vdw 2.248 3.540 nonbonded pdb=" NZ LYS N 128 " pdb=" O PRO O 136 " model vdw 2.257 3.120 nonbonded pdb=" O VAL H 203 " pdb=" OG SER H 257 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG H 136 " pdb=" O HIS I 32 " model vdw 2.304 3.120 ... (remaining 75648 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.930 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.250 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 10036 Z= 0.378 Angle : 1.008 9.753 13644 Z= 0.593 Chirality : 0.063 0.348 1563 Planarity : 0.007 0.064 1745 Dihedral : 11.464 74.505 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.27 % Favored : 87.48 % Rotamer: Outliers : 1.08 % Allowed : 3.11 % Favored : 95.81 % Cbeta Deviations : 0.08 % 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: -5.06 (0.18), residues: 1214 helix: -3.16 (0.16), residues: 405 sheet: -2.66 (0.48), residues: 93 loop : -3.76 (0.19), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.008 0.001 HIS M 169 PHE 0.016 0.002 PHE H 182 TYR 0.016 0.002 TYR J 57 ARG 0.015 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 262 time to evaluate : 1.100 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE H 132 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.7825 (tpt) cc_final: 0.7336 (tpp) REVERT: H 47 LEU cc_start: 0.9296 (tp) cc_final: 0.8851 (tp) REVERT: H 49 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7844 (mpp80) REVERT: H 105 MET cc_start: 0.9533 (ptp) cc_final: 0.9057 (ptt) REVERT: H 156 ASN cc_start: 0.9382 (t0) cc_final: 0.9130 (t0) REVERT: H 171 TRP cc_start: 0.9322 (t60) cc_final: 0.9042 (t60) REVERT: H 261 TYR cc_start: 0.8837 (t80) cc_final: 0.8626 (t80) REVERT: H 262 LEU cc_start: 0.9547 (mt) cc_final: 0.9286 (pp) REVERT: H 378 MET cc_start: 0.9076 (mmp) cc_final: 0.8669 (mmp) REVERT: H 381 LEU cc_start: 0.9450 (pp) cc_final: 0.8455 (pp) REVERT: H 384 ILE cc_start: 0.9671 (mm) cc_final: 0.9321 (tp) REVERT: H 390 GLU cc_start: 0.9130 (pt0) cc_final: 0.8798 (pt0) REVERT: I 85 LEU cc_start: 0.8474 (mt) cc_final: 0.7835 (tp) REVERT: I 100 ASP cc_start: 0.8560 (t0) cc_final: 0.7633 (t70) REVERT: I 101 PHE cc_start: 0.9240 (m-10) cc_final: 0.8995 (m-80) REVERT: I 103 ILE cc_start: 0.9528 (mm) cc_final: 0.9170 (mm) REVERT: I 134 GLU cc_start: 0.8639 (tt0) cc_final: 0.8424 (tm-30) REVERT: I 137 TYR cc_start: 0.7528 (m-10) cc_final: 0.6809 (m-10) REVERT: J 51 LEU cc_start: 0.8577 (tp) cc_final: 0.8373 (tp) REVERT: J 71 LEU cc_start: 0.8562 (tp) cc_final: 0.8171 (tp) REVERT: J 111 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8535 (mm-30) REVERT: J 128 LEU cc_start: 0.8978 (tp) cc_final: 0.8569 (mt) REVERT: K 103 ILE cc_start: 0.9291 (mm) cc_final: 0.8892 (mp) REVERT: K 144 GLU cc_start: 0.8132 (mp0) cc_final: 0.7815 (tp30) REVERT: L 128 MET cc_start: 0.8939 (mmm) cc_final: 0.8601 (mmt) REVERT: L 142 LEU cc_start: 0.8682 (mm) cc_final: 0.8471 (mm) REVERT: L 144 LEU cc_start: 0.8174 (pt) cc_final: 0.7949 (pt) REVERT: L 160 MET cc_start: 0.7307 (mpp) cc_final: 0.6776 (tpp) REVERT: N 140 VAL cc_start: 0.9093 (m) cc_final: 0.8871 (p) outliers start: 9 outliers final: 3 residues processed: 268 average time/residue: 0.2411 time to fit residues: 87.5394 Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 48 HIS H 363 GLN J 110 GLN ** M 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.055550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050193 restraints weight = 119933.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051010 restraints weight = 79629.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.051592 restraints weight = 57471.382| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10036 Z= 0.417 Angle : 0.887 11.798 13644 Z= 0.462 Chirality : 0.053 0.371 1563 Planarity : 0.007 0.071 1745 Dihedral : 6.191 25.890 1452 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.45 % Favored : 88.47 % Rotamer: Outliers : 0.48 % Allowed : 5.50 % Favored : 94.02 % 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: -3.64 (0.21), residues: 1214 helix: -1.31 (0.22), residues: 422 sheet: -2.75 (0.42), residues: 111 loop : -3.23 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 350 HIS 0.017 0.003 HIS M 96 PHE 0.021 0.002 PHE K 115 TYR 0.016 0.002 TYR O 127 ARG 0.008 0.001 ARG J 112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8463 (tpt) cc_final: 0.8009 (tpp) REVERT: H 76 MET cc_start: 0.8984 (mtt) cc_final: 0.8569 (mtm) REVERT: H 105 MET cc_start: 0.9418 (ptp) cc_final: 0.9161 (ptp) REVERT: H 223 MET cc_start: 0.9347 (mpp) cc_final: 0.9112 (mpp) REVERT: I 9 MET cc_start: 0.1860 (tmm) cc_final: 0.1599 (tmm) REVERT: I 85 LEU cc_start: 0.9095 (mt) cc_final: 0.8683 (tp) REVERT: I 100 ASP cc_start: 0.8902 (t0) cc_final: 0.8133 (t70) REVERT: I 101 PHE cc_start: 0.9090 (m-10) cc_final: 0.8543 (m-80) REVERT: I 103 ILE cc_start: 0.9686 (mm) cc_final: 0.9451 (mm) REVERT: I 135 LEU cc_start: 0.9325 (mp) cc_final: 0.9051 (mp) REVERT: I 137 TYR cc_start: 0.8024 (m-10) cc_final: 0.7497 (m-10) REVERT: J 86 ILE cc_start: 0.9384 (mp) cc_final: 0.9116 (tt) REVERT: J 133 MET cc_start: 0.8947 (mmm) cc_final: 0.8703 (mmm) REVERT: J 151 PHE cc_start: 0.8872 (m-80) cc_final: 0.8461 (m-80) REVERT: K 105 MET cc_start: 0.8208 (ptp) cc_final: 0.7980 (ptp) REVERT: K 114 MET cc_start: 0.9016 (pmm) cc_final: 0.8712 (pmm) REVERT: K 136 LEU cc_start: 0.9108 (tp) cc_final: 0.8847 (tp) REVERT: K 144 GLU cc_start: 0.8818 (mp0) cc_final: 0.8060 (tp30) REVERT: K 148 ASP cc_start: 0.8557 (m-30) cc_final: 0.7780 (m-30) REVERT: L 128 MET cc_start: 0.8987 (mmm) cc_final: 0.8587 (mmt) REVERT: L 144 LEU cc_start: 0.8563 (pt) cc_final: 0.8170 (pt) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 0.1995 time to fit residues: 52.2615 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS H 93 GLN H 361 ASN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.054101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049022 restraints weight = 122360.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.049770 restraints weight = 80173.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.050326 restraints weight = 57641.987| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10036 Z= 0.374 Angle : 0.806 8.947 13644 Z= 0.421 Chirality : 0.049 0.207 1563 Planarity : 0.008 0.118 1745 Dihedral : 6.223 27.735 1452 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.34 % Favored : 86.57 % Rotamer: Outliers : 0.48 % Allowed : 5.38 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 1214 helix: -1.02 (0.23), residues: 459 sheet: -2.93 (0.46), residues: 93 loop : -3.04 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 171 HIS 0.013 0.003 HIS H 114 PHE 0.026 0.002 PHE H 340 TYR 0.025 0.002 TYR J 69 ARG 0.010 0.001 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8942 (tpt) cc_final: 0.8558 (tpp) REVERT: H 76 MET cc_start: 0.8893 (mtt) cc_final: 0.8644 (ttm) REVERT: H 105 MET cc_start: 0.9371 (ptp) cc_final: 0.8917 (ptt) REVERT: H 154 MET cc_start: 0.7386 (mtt) cc_final: 0.6884 (mtt) REVERT: H 223 MET cc_start: 0.9308 (mpp) cc_final: 0.8974 (mpp) REVERT: H 262 LEU cc_start: 0.9719 (mt) cc_final: 0.9404 (pp) REVERT: H 340 PHE cc_start: 0.8946 (t80) cc_final: 0.8524 (t80) REVERT: H 390 GLU cc_start: 0.9192 (pt0) cc_final: 0.8788 (pt0) REVERT: I 100 ASP cc_start: 0.8822 (t0) cc_final: 0.8374 (t70) REVERT: I 103 ILE cc_start: 0.9640 (mm) cc_final: 0.9358 (mm) REVERT: J 70 HIS cc_start: 0.8069 (m90) cc_final: 0.7861 (m90) REVERT: J 133 MET cc_start: 0.9214 (mmm) cc_final: 0.8781 (mmm) REVERT: J 151 PHE cc_start: 0.9142 (m-80) cc_final: 0.8795 (m-80) REVERT: K 37 LEU cc_start: 0.7153 (tp) cc_final: 0.6938 (tp) REVERT: K 85 MET cc_start: 0.9040 (mmp) cc_final: 0.8767 (mmm) REVERT: K 114 MET cc_start: 0.8879 (pmm) cc_final: 0.8438 (pmm) REVERT: K 144 GLU cc_start: 0.8909 (mp0) cc_final: 0.7826 (tp30) REVERT: K 148 ASP cc_start: 0.8759 (m-30) cc_final: 0.7717 (m-30) REVERT: L 108 MET cc_start: 0.8981 (mpp) cc_final: 0.8612 (mpp) REVERT: L 128 MET cc_start: 0.9037 (mmm) cc_final: 0.8592 (mmt) REVERT: M 100 TYR cc_start: 0.8703 (m-80) cc_final: 0.8401 (m-80) outliers start: 4 outliers final: 4 residues processed: 158 average time/residue: 0.1928 time to fit residues: 44.4635 Evaluate side-chains 131 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.057786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052559 restraints weight = 116248.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.053367 restraints weight = 75247.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.053955 restraints weight = 53909.824| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10036 Z= 0.180 Angle : 0.657 11.641 13644 Z= 0.329 Chirality : 0.046 0.180 1563 Planarity : 0.006 0.096 1745 Dihedral : 5.367 24.619 1452 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 0.36 % Allowed : 3.95 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.86 (0.24), residues: 1214 helix: -0.57 (0.24), residues: 469 sheet: -2.92 (0.42), residues: 108 loop : -2.84 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 35 HIS 0.008 0.001 HIS H 155 PHE 0.021 0.001 PHE K 115 TYR 0.018 0.001 TYR K 93 ARG 0.005 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8616 (tpt) cc_final: 0.8140 (tpp) REVERT: H 47 LEU cc_start: 0.9611 (tp) cc_final: 0.9321 (tp) REVERT: H 76 MET cc_start: 0.8749 (mtt) cc_final: 0.8482 (mtm) REVERT: H 154 MET cc_start: 0.6927 (mtt) cc_final: 0.6096 (mtt) REVERT: H 171 TRP cc_start: 0.9165 (t60) cc_final: 0.8920 (t60) REVERT: H 223 MET cc_start: 0.9120 (mpp) cc_final: 0.8813 (mpp) REVERT: H 262 LEU cc_start: 0.9727 (mt) cc_final: 0.9378 (pp) REVERT: H 340 PHE cc_start: 0.8930 (t80) cc_final: 0.8554 (t80) REVERT: H 390 GLU cc_start: 0.9223 (pt0) cc_final: 0.8846 (pt0) REVERT: I 85 LEU cc_start: 0.8925 (mt) cc_final: 0.8285 (tp) REVERT: I 100 ASP cc_start: 0.8916 (t0) cc_final: 0.8374 (t70) REVERT: I 103 ILE cc_start: 0.9703 (mm) cc_final: 0.9479 (mm) REVERT: I 137 TYR cc_start: 0.8257 (m-80) cc_final: 0.7804 (m-10) REVERT: J 133 MET cc_start: 0.9169 (mmm) cc_final: 0.8766 (mmm) REVERT: J 151 PHE cc_start: 0.9167 (m-80) cc_final: 0.8660 (m-80) REVERT: K 85 MET cc_start: 0.8929 (mmp) cc_final: 0.8714 (mmp) REVERT: K 114 MET cc_start: 0.9022 (pmm) cc_final: 0.8445 (pmm) REVERT: K 136 LEU cc_start: 0.8876 (tp) cc_final: 0.8638 (tt) REVERT: K 144 GLU cc_start: 0.8904 (mp0) cc_final: 0.7870 (tp30) REVERT: K 148 ASP cc_start: 0.8654 (m-30) cc_final: 0.7790 (m-30) REVERT: L 128 MET cc_start: 0.9057 (mmm) cc_final: 0.8716 (mmt) REVERT: M 100 TYR cc_start: 0.8627 (m-80) cc_final: 0.8393 (m-80) REVERT: N 108 LEU cc_start: 0.8991 (tp) cc_final: 0.8664 (tt) outliers start: 3 outliers final: 3 residues processed: 176 average time/residue: 0.1962 time to fit residues: 49.9351 Evaluate side-chains 147 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 18 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.048286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.042483 restraints weight = 117501.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043094 restraints weight = 85237.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043638 restraints weight = 67090.987| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10036 Z= 0.206 Angle : 0.659 11.485 13644 Z= 0.332 Chirality : 0.046 0.177 1563 Planarity : 0.005 0.066 1745 Dihedral : 5.239 24.122 1452 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 0.36 % Allowed : 2.15 % Favored : 97.49 % 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: -2.66 (0.24), residues: 1214 helix: -0.42 (0.24), residues: 467 sheet: -2.60 (0.46), residues: 98 loop : -2.75 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 35 HIS 0.005 0.001 HIS H 155 PHE 0.020 0.001 PHE K 115 TYR 0.021 0.001 TYR K 135 ARG 0.004 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8771 (tpt) cc_final: 0.8323 (tpp) REVERT: H 47 LEU cc_start: 0.9603 (tp) cc_final: 0.9267 (tp) REVERT: H 79 GLU cc_start: 0.8918 (tt0) cc_final: 0.7888 (mm-30) REVERT: H 171 TRP cc_start: 0.9310 (t60) cc_final: 0.9081 (t60) REVERT: H 208 ILE cc_start: 0.9219 (pt) cc_final: 0.8796 (mm) REVERT: H 223 MET cc_start: 0.9114 (mpp) cc_final: 0.8820 (mpp) REVERT: H 262 LEU cc_start: 0.9740 (mt) cc_final: 0.9417 (pp) REVERT: H 340 PHE cc_start: 0.8752 (t80) cc_final: 0.8442 (t80) REVERT: H 390 GLU cc_start: 0.9150 (pt0) cc_final: 0.8830 (pt0) REVERT: I 85 LEU cc_start: 0.9052 (mt) cc_final: 0.8088 (tp) REVERT: I 100 ASP cc_start: 0.8866 (t0) cc_final: 0.8254 (t70) REVERT: I 103 ILE cc_start: 0.9627 (mm) cc_final: 0.9254 (mm) REVERT: I 137 TYR cc_start: 0.8206 (m-80) cc_final: 0.7660 (m-80) REVERT: J 133 MET cc_start: 0.9217 (mmm) cc_final: 0.8894 (mmm) REVERT: J 151 PHE cc_start: 0.9128 (m-80) cc_final: 0.8655 (m-80) REVERT: K 85 MET cc_start: 0.8789 (mmp) cc_final: 0.8541 (mmp) REVERT: K 114 MET cc_start: 0.9101 (pmm) cc_final: 0.8346 (pmm) REVERT: K 144 GLU cc_start: 0.9039 (mp0) cc_final: 0.7920 (tp30) REVERT: K 148 ASP cc_start: 0.8924 (m-30) cc_final: 0.7638 (m-30) REVERT: L 108 MET cc_start: 0.9004 (mpp) cc_final: 0.8542 (mpp) REVERT: L 128 MET cc_start: 0.9161 (mmm) cc_final: 0.8723 (mmt) REVERT: M 100 TYR cc_start: 0.8698 (m-10) cc_final: 0.8481 (m-80) REVERT: N 108 LEU cc_start: 0.8995 (tp) cc_final: 0.8667 (tt) outliers start: 3 outliers final: 3 residues processed: 172 average time/residue: 0.2206 time to fit residues: 54.8417 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 60 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.052154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.047424 restraints weight = 124981.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048171 restraints weight = 81111.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.048701 restraints weight = 57507.020| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.8607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 10036 Z= 0.458 Angle : 0.897 11.068 13644 Z= 0.467 Chirality : 0.052 0.203 1563 Planarity : 0.007 0.077 1745 Dihedral : 6.683 31.143 1452 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 28.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.83 % Favored : 85.01 % Rotamer: Outliers : 0.36 % Allowed : 4.55 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.30 (0.23), residues: 1214 helix: -1.13 (0.23), residues: 459 sheet: -2.99 (0.50), residues: 84 loop : -2.97 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP K 35 HIS 0.014 0.003 HIS H 155 PHE 0.028 0.002 PHE K 115 TYR 0.025 0.002 TYR K 93 ARG 0.013 0.001 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.9207 (tpt) cc_final: 0.8628 (tpp) REVERT: H 47 LEU cc_start: 0.9606 (tp) cc_final: 0.9387 (tp) REVERT: H 154 MET cc_start: 0.6797 (mtt) cc_final: 0.6270 (mtt) REVERT: H 171 TRP cc_start: 0.9369 (t60) cc_final: 0.9151 (t60) REVERT: H 340 PHE cc_start: 0.9079 (t80) cc_final: 0.8600 (t80) REVERT: H 352 TRP cc_start: 0.9201 (t-100) cc_final: 0.8643 (t-100) REVERT: H 390 GLU cc_start: 0.9270 (pt0) cc_final: 0.9055 (pt0) REVERT: I 100 ASP cc_start: 0.8996 (t0) cc_final: 0.8367 (t70) REVERT: I 103 ILE cc_start: 0.9647 (mm) cc_final: 0.9394 (mm) REVERT: I 137 TYR cc_start: 0.8378 (m-80) cc_final: 0.8029 (m-10) REVERT: J 70 HIS cc_start: 0.8164 (m90) cc_final: 0.7949 (m90) REVERT: J 133 MET cc_start: 0.9305 (mmm) cc_final: 0.8791 (mmm) REVERT: K 85 MET cc_start: 0.8939 (mmp) cc_final: 0.8619 (mmm) REVERT: L 108 MET cc_start: 0.9038 (mpp) cc_final: 0.8737 (mpp) REVERT: L 128 MET cc_start: 0.9049 (mmm) cc_final: 0.8733 (mmt) outliers start: 3 outliers final: 3 residues processed: 143 average time/residue: 0.1892 time to fit residues: 39.6255 Evaluate side-chains 114 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN H 363 GLN M 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.047545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.041934 restraints weight = 113445.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.042608 restraints weight = 81601.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043003 restraints weight = 63567.254| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.8027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10036 Z= 0.187 Angle : 0.691 11.610 13644 Z= 0.342 Chirality : 0.046 0.161 1563 Planarity : 0.005 0.074 1745 Dihedral : 5.559 25.190 1452 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.38 % Favored : 89.54 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.33 % 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: -2.83 (0.23), residues: 1214 helix: -0.55 (0.24), residues: 464 sheet: -2.82 (0.45), residues: 93 loop : -2.84 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 247 HIS 0.006 0.001 HIS H 114 PHE 0.017 0.001 PHE I 101 TYR 0.020 0.001 TYR K 93 ARG 0.007 0.001 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8865 (tpt) cc_final: 0.8441 (tpp) REVERT: H 154 MET cc_start: 0.6195 (mtt) cc_final: 0.5712 (mtt) REVERT: H 171 TRP cc_start: 0.9397 (t60) cc_final: 0.9196 (t60) REVERT: H 208 ILE cc_start: 0.9302 (pt) cc_final: 0.8925 (mm) REVERT: H 262 LEU cc_start: 0.9690 (mt) cc_final: 0.9406 (pp) REVERT: H 340 PHE cc_start: 0.8940 (t80) cc_final: 0.8586 (t80) REVERT: H 352 TRP cc_start: 0.9026 (t-100) cc_final: 0.8718 (t-100) REVERT: H 390 GLU cc_start: 0.9221 (pt0) cc_final: 0.8905 (pt0) REVERT: I 100 ASP cc_start: 0.9036 (t0) cc_final: 0.8326 (t70) REVERT: I 101 PHE cc_start: 0.9196 (m-10) cc_final: 0.8984 (m-10) REVERT: I 103 ILE cc_start: 0.9703 (mm) cc_final: 0.9463 (mm) REVERT: J 50 TYR cc_start: 0.8032 (t80) cc_final: 0.7534 (t80) REVERT: J 133 MET cc_start: 0.9389 (mmm) cc_final: 0.9008 (mmm) REVERT: K 37 LEU cc_start: 0.8482 (tt) cc_final: 0.8019 (tp) REVERT: L 108 MET cc_start: 0.9200 (mpp) cc_final: 0.8586 (mpp) REVERT: L 128 MET cc_start: 0.9182 (mmm) cc_final: 0.8815 (mmt) REVERT: N 108 LEU cc_start: 0.9316 (tp) cc_final: 0.9002 (tt) outliers start: 3 outliers final: 3 residues processed: 165 average time/residue: 0.1899 time to fit residues: 46.2727 Evaluate side-chains 137 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.046433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040844 restraints weight = 120542.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041533 restraints weight = 85469.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042065 restraints weight = 65207.397| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.8206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10036 Z= 0.228 Angle : 0.691 10.965 13644 Z= 0.346 Chirality : 0.046 0.143 1563 Planarity : 0.005 0.073 1745 Dihedral : 5.496 24.906 1452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.44 % Favored : 87.48 % Rotamer: Outliers : 0.36 % Allowed : 1.32 % Favored : 98.33 % 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: -2.83 (0.23), residues: 1214 helix: -0.58 (0.23), residues: 480 sheet: -2.75 (0.46), residues: 93 loop : -2.88 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 247 HIS 0.008 0.001 HIS H 114 PHE 0.020 0.001 PHE L 134 TYR 0.020 0.002 TYR K 93 ARG 0.008 0.001 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.9053 (tpt) cc_final: 0.8602 (tpp) REVERT: H 79 GLU cc_start: 0.9099 (tt0) cc_final: 0.8683 (tt0) REVERT: H 154 MET cc_start: 0.6154 (mtt) cc_final: 0.5615 (mtt) REVERT: H 171 TRP cc_start: 0.9408 (t60) cc_final: 0.9203 (t60) REVERT: H 208 ILE cc_start: 0.9267 (pt) cc_final: 0.8873 (mm) REVERT: H 262 LEU cc_start: 0.9729 (mt) cc_final: 0.9433 (pp) REVERT: H 340 PHE cc_start: 0.8793 (t80) cc_final: 0.8328 (t80) REVERT: H 352 TRP cc_start: 0.8987 (t-100) cc_final: 0.8771 (t-100) REVERT: H 390 GLU cc_start: 0.9273 (pt0) cc_final: 0.8940 (pt0) REVERT: I 100 ASP cc_start: 0.9066 (t0) cc_final: 0.8243 (t0) REVERT: I 103 ILE cc_start: 0.9668 (mm) cc_final: 0.9387 (mm) REVERT: I 106 PHE cc_start: 0.8915 (m-80) cc_final: 0.8681 (m-10) REVERT: J 50 TYR cc_start: 0.8156 (t80) cc_final: 0.7554 (t80) REVERT: J 57 TYR cc_start: 0.7792 (p90) cc_final: 0.7400 (p90) REVERT: J 133 MET cc_start: 0.9302 (mmm) cc_final: 0.8913 (mmm) REVERT: K 37 LEU cc_start: 0.8424 (tt) cc_final: 0.7979 (tp) REVERT: K 96 MET cc_start: 0.6941 (mmm) cc_final: 0.6628 (mmt) REVERT: L 108 MET cc_start: 0.9185 (mpp) cc_final: 0.8654 (mpp) REVERT: L 128 MET cc_start: 0.9177 (mmm) cc_final: 0.8765 (mmt) REVERT: M 161 ARG cc_start: 0.9078 (ptp-170) cc_final: 0.8531 (ptp-170) REVERT: N 108 LEU cc_start: 0.9202 (tp) cc_final: 0.8911 (tt) outliers start: 3 outliers final: 3 residues processed: 162 average time/residue: 0.1793 time to fit residues: 43.4810 Evaluate side-chains 135 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.047776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.041975 restraints weight = 113024.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.042701 restraints weight = 80824.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043223 restraints weight = 62434.105| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10036 Z= 0.176 Angle : 0.668 10.962 13644 Z= 0.328 Chirality : 0.046 0.150 1563 Planarity : 0.005 0.057 1745 Dihedral : 5.170 22.987 1452 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.80 % Favored : 90.12 % Rotamer: Outliers : 0.36 % Allowed : 1.20 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.24), residues: 1214 helix: -0.44 (0.24), residues: 480 sheet: -2.42 (0.48), residues: 93 loop : -2.78 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 217 HIS 0.006 0.001 HIS H 114 PHE 0.015 0.001 PHE H 182 TYR 0.019 0.001 TYR M 100 ARG 0.005 0.001 ARG I 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8844 (tpt) cc_final: 0.8390 (tpp) REVERT: H 47 LEU cc_start: 0.9632 (tp) cc_final: 0.9431 (tp) REVERT: H 79 GLU cc_start: 0.9110 (tt0) cc_final: 0.8366 (mm-30) REVERT: H 154 MET cc_start: 0.5608 (mtt) cc_final: 0.4963 (mtt) REVERT: H 171 TRP cc_start: 0.9371 (t60) cc_final: 0.9163 (t60) REVERT: H 208 ILE cc_start: 0.9220 (pt) cc_final: 0.8834 (mm) REVERT: H 262 LEU cc_start: 0.9720 (mt) cc_final: 0.9400 (pp) REVERT: H 340 PHE cc_start: 0.8807 (t80) cc_final: 0.8504 (t80) REVERT: H 390 GLU cc_start: 0.9335 (pt0) cc_final: 0.8991 (pt0) REVERT: I 100 ASP cc_start: 0.9010 (t0) cc_final: 0.8296 (t70) REVERT: I 103 ILE cc_start: 0.9645 (mm) cc_final: 0.9393 (mm) REVERT: I 106 PHE cc_start: 0.8848 (m-80) cc_final: 0.8598 (m-10) REVERT: J 50 TYR cc_start: 0.8014 (t80) cc_final: 0.7481 (t80) REVERT: J 133 MET cc_start: 0.9249 (mmm) cc_final: 0.8895 (mmm) REVERT: K 37 LEU cc_start: 0.8194 (tt) cc_final: 0.7801 (tp) REVERT: K 85 MET cc_start: 0.8958 (mmp) cc_final: 0.8611 (mmp) REVERT: K 144 GLU cc_start: 0.9092 (pm20) cc_final: 0.8832 (pm20) REVERT: K 148 ASP cc_start: 0.9177 (m-30) cc_final: 0.8695 (m-30) REVERT: L 128 MET cc_start: 0.9203 (mmm) cc_final: 0.8734 (mmt) REVERT: L 144 LEU cc_start: 0.7815 (tp) cc_final: 0.7431 (pp) REVERT: M 100 TYR cc_start: 0.8692 (m-80) cc_final: 0.8388 (m-80) REVERT: N 108 LEU cc_start: 0.9209 (tp) cc_final: 0.8958 (tt) outliers start: 3 outliers final: 3 residues processed: 169 average time/residue: 0.1920 time to fit residues: 48.6488 Evaluate side-chains 140 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 70 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 0.0060 chunk 24 optimal weight: 10.0000 chunk 1 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.047908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.042124 restraints weight = 112239.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.042802 restraints weight = 81349.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043377 restraints weight = 63150.446| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10036 Z= 0.169 Angle : 0.673 12.993 13644 Z= 0.327 Chirality : 0.045 0.152 1563 Planarity : 0.005 0.047 1745 Dihedral : 4.961 21.991 1452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.46 % Favored : 89.46 % Rotamer: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.60 (0.24), residues: 1214 helix: -0.40 (0.24), residues: 490 sheet: -2.33 (0.48), residues: 93 loop : -2.82 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP M 131 HIS 0.006 0.001 HIS H 114 PHE 0.020 0.001 PHE L 134 TYR 0.018 0.001 TYR M 100 ARG 0.005 0.001 ARG I 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 15 MET cc_start: 0.8769 (tpt) cc_final: 0.8460 (tpp) REVERT: H 47 LEU cc_start: 0.9616 (tp) cc_final: 0.9377 (tp) REVERT: H 79 GLU cc_start: 0.9057 (tt0) cc_final: 0.8196 (mm-30) REVERT: H 154 MET cc_start: 0.5430 (mtt) cc_final: 0.4673 (mtt) REVERT: H 208 ILE cc_start: 0.9170 (pt) cc_final: 0.8799 (mm) REVERT: H 340 PHE cc_start: 0.8789 (t80) cc_final: 0.8467 (t80) REVERT: H 378 MET cc_start: 0.8904 (mmp) cc_final: 0.8278 (mmt) REVERT: H 390 GLU cc_start: 0.9214 (pt0) cc_final: 0.8798 (pt0) REVERT: I 100 ASP cc_start: 0.8993 (t0) cc_final: 0.8334 (t70) REVERT: I 103 ILE cc_start: 0.9654 (mm) cc_final: 0.9425 (mm) REVERT: I 106 PHE cc_start: 0.8650 (m-80) cc_final: 0.8441 (m-10) REVERT: I 125 TYR cc_start: 0.8628 (p90) cc_final: 0.8054 (p90) REVERT: J 50 TYR cc_start: 0.7901 (t80) cc_final: 0.7378 (t80) REVERT: J 133 MET cc_start: 0.9243 (mmm) cc_final: 0.8827 (mmm) REVERT: K 37 LEU cc_start: 0.8095 (tt) cc_final: 0.7712 (tp) REVERT: K 69 PRO cc_start: 0.7502 (Cg_endo) cc_final: 0.7171 (Cg_exo) REVERT: K 85 MET cc_start: 0.9097 (mmp) cc_final: 0.8659 (mmp) REVERT: L 128 MET cc_start: 0.9201 (mmm) cc_final: 0.8758 (mmt) REVERT: M 100 TYR cc_start: 0.8670 (m-80) cc_final: 0.8303 (m-80) REVERT: M 161 ARG cc_start: 0.9092 (ptp-170) cc_final: 0.8723 (ptt-90) REVERT: N 108 LEU cc_start: 0.8907 (tp) cc_final: 0.8611 (tt) outliers start: 3 outliers final: 3 residues processed: 169 average time/residue: 0.1882 time to fit residues: 47.1854 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 74 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 6 optimal weight: 0.0980 chunk 2 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.042665 restraints weight = 107128.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.043319 restraints weight = 78360.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.043714 restraints weight = 62173.947| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.8052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10036 Z= 0.169 Angle : 0.667 12.821 13644 Z= 0.326 Chirality : 0.045 0.162 1563 Planarity : 0.005 0.047 1745 Dihedral : 4.897 21.395 1452 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.88 % Favored : 90.03 % Rotamer: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.52 (0.24), residues: 1214 helix: -0.31 (0.24), residues: 476 sheet: -2.43 (0.47), residues: 99 loop : -2.72 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 131 HIS 0.008 0.001 HIS M 96 PHE 0.009 0.001 PHE L 134 TYR 0.023 0.001 TYR K 39 ARG 0.005 0.000 ARG I 17 =============================================================================== Job complete usr+sys time: 2909.22 seconds wall clock time: 53 minutes 57.19 seconds (3237.19 seconds total)