Starting phenix.real_space_refine on Sat May 2 23:04:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnb_48419/05_2026/9mnb_48419.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5552 2.51 5 N 1499 2.21 5 O 1733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8815 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1644 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "A" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1739 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 17, 'TRANS': 201} Chain breaks: 1 Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1600 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1641 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1586 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Chain: "K" Number of atoms: 605 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 600 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'TRANS': 119} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 Conformer: "B" Number of residues, atoms: 120, 600 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'TRANS': 119} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 bond proxies already assigned to first conformer: 593 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AUNK K 46 " occ=0.60 ... (8 atoms not shown) pdb=" CB BUNK K 46 " occ=0.40 Time building chain proxies: 2.55, per 1000 atoms: 0.29 Number of scatterers: 8815 At special positions: 0 Unit cell: (77.096, 91.342, 204.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1733 8.00 N 1499 7.00 C 5552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 182 " distance=2.02 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 196 " distance=2.03 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: 0.89 Conformation dependent library (CDL) restraints added in 363.7 milliseconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 28 sheets defined 13.4% alpha, 51.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'L' and resid 28 through 31 removed outlier: 4.382A pdb=" N ASN L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.536A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 60 through 60D removed outlier: 3.614A pdb=" N LYS A 60D" --> pdb=" O PRO A 60A" (cutoff:3.500A) Processing helix chain 'A' and resid 60E through 63 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 164 through 173A Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.657A pdb=" N HIS A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.408A pdb=" N GLY H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 153 through 158 Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.954A pdb=" N ALA F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.969A pdb=" N ARG E 66 " --> pdb=" O TRP E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.618A pdb=" N LEU E 189 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.679A pdb=" N UNK K 64 " --> pdb=" O UNK K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.649A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.649A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR L 97 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 118 removed outlier: 4.018A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.455A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.813A pdb=" N VAL A 31 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY A 43 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 33 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 105 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 88 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU A 107 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 135 through 140 removed outlier: 3.810A pdb=" N LYS A 156 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS A 182 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 227 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 199 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 139 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 202 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.604A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.877A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.614A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.614A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'H' and resid 194 through 195 removed outlier: 4.213A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.515A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.054A pdb=" N VAL F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 107 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU F 13 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN F 50 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.054A pdb=" N VAL F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS F 107 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU F 13 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 115 through 118 removed outlier: 4.073A pdb=" N VAL F 133 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASN F 138 " --> pdb=" O TYR F 173 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.939A pdb=" N TYR F 192 " --> pdb=" O PHE F 209 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.733A pdb=" N ARG E 8 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR E 21 " --> pdb=" O ARG E 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 82 " --> pdb=" O LEU E 18 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.153A pdb=" N ASP E 33 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.895A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.026A pdb=" N TYR E 176 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.026A pdb=" N TYR E 176 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 195 through 200 removed outlier: 3.691A pdb=" N VAL E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.660A pdb=" N UNK K 38 " --> pdb=" O UNK K 47 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N UNK K 47 " --> pdb=" O UNK K 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.534A pdb=" N UNK K 102 " --> pdb=" O UNK K 94 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 948 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: 1.61 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2846 1.34 - 1.46: 2033 1.46 - 1.58: 4097 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 9014 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LYS A 26 " pdb=" CA LYS A 26 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ILE L 2 " pdb=" CA ILE L 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N VAL H 2 " pdb=" CA VAL H 2 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.67e+00 bond pdb=" CA UNK K 100B" pdb=" CB UNK K 100B" ideal model delta sigma weight residual 1.530 1.499 0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 9009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 11298 1.31 - 2.61: 854 2.61 - 3.92: 133 3.92 - 5.23: 31 5.23 - 6.53: 7 Bond angle restraints: 12323 Sorted by residual: angle pdb=" N GLN F 50 " pdb=" CA GLN F 50 " pdb=" C GLN F 50 " ideal model delta sigma weight residual 109.24 104.40 4.84 1.51e+00 4.39e-01 1.03e+01 angle pdb=" C SER H 25 " pdb=" N ARG H 26 " pdb=" CA ARG H 26 " ideal model delta sigma weight residual 121.54 127.30 -5.76 1.91e+00 2.74e-01 9.08e+00 angle pdb=" N GLY F 101 " pdb=" CA GLY F 101 " pdb=" C GLY F 101 " ideal model delta sigma weight residual 111.93 115.14 -3.21 1.15e+00 7.56e-01 7.77e+00 angle pdb=" C UNK K 53 " pdb=" N UNK K 54 " pdb=" CA UNK K 54 " ideal model delta sigma weight residual 121.70 126.63 -4.93 1.80e+00 3.09e-01 7.51e+00 angle pdb=" C UNK K 64 " pdb=" N UNK K 65 " pdb=" CA UNK K 65 " ideal model delta sigma weight residual 121.70 126.44 -4.74 1.80e+00 3.09e-01 6.93e+00 ... (remaining 12318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5051 17.99 - 35.98: 258 35.98 - 53.98: 45 53.98 - 71.97: 16 71.97 - 89.96: 9 Dihedral angle restraints: 5379 sinusoidal: 1906 harmonic: 3473 Sorted by residual: dihedral pdb=" CA THR E 68 " pdb=" C THR E 68 " pdb=" N ILE E 69 " pdb=" CA ILE E 69 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLN F 50 " pdb=" C GLN F 50 " pdb=" N ALA F 51 " pdb=" CA ALA F 51 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA TRP F 148 " pdb=" C TRP F 148 " pdb=" N LYS F 149 " pdb=" CA LYS F 149 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 5376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 918 0.041 - 0.082: 371 0.082 - 0.123: 123 0.123 - 0.164: 26 0.164 - 0.205: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA UNK K 100B" pdb=" N UNK K 100B" pdb=" C UNK K 100B" pdb=" CB UNK K 100B" both_signs ideal model delta sigma weight residual False 2.52 2.32 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" C PRO L 80 " pdb=" CB PRO L 80 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1436 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 71 " -0.229 9.50e-02 1.11e+02 1.03e-01 6.86e+00 pdb=" NE ARG E 71 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 71 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG E 71 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 71 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 97 " 0.193 9.50e-02 1.11e+02 8.73e-02 6.35e+00 pdb=" NE ARG H 97 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG H 97 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG H 97 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 97 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 38 " 0.204 9.50e-02 1.11e+02 9.20e-02 6.25e+00 pdb=" NE ARG H 38 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 38 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG H 38 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 38 " 0.001 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 25 2.54 - 3.13: 6818 3.13 - 3.72: 12680 3.72 - 4.31: 18857 4.31 - 4.90: 31987 Nonbonded interactions: 70367 Sorted by model distance: nonbonded pdb=" CG2 THR L 197 " pdb=" O UNK K 100A" model vdw 1.949 3.460 nonbonded pdb=" OH TYR E 145 " pdb=" OE1 GLU E 148 " model vdw 2.314 3.040 nonbonded pdb=" O GLN F 50 " pdb=" N SER F 52 " model vdw 2.326 3.120 nonbonded pdb=" OH TYR L 36 " pdb=" O LEU H 100C" model vdw 2.387 3.040 nonbonded pdb=" O ASN L 137 " pdb=" OG SER L 174 " model vdw 2.394 3.040 ... (remaining 70362 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=0.40 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: 8.840 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 0.039 9026 Z= 0.255 Angle : 0.775 6.533 12347 Z= 0.425 Chirality : 0.049 0.205 1439 Planarity : 0.008 0.103 1578 Dihedral : 12.714 89.960 3109 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.23 % Favored : 95.58 % Rotamer: Outliers : 0.97 % Allowed : 3.79 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1063 helix: -3.06 (0.46), residues: 51 sheet: 0.56 (0.25), residues: 401 loop : -0.30 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.004 ARG H 97 TYR 0.028 0.005 TYR L 29 PHE 0.012 0.003 PHE E 146 TRP 0.023 0.004 TRP H 103 HIS 0.015 0.003 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 9014) covalent geometry : angle 0.77461 (12323) SS BOND : bond 0.00568 ( 12) SS BOND : angle 0.97767 ( 24) hydrogen bonds : bond 0.18687 ( 346) hydrogen bonds : angle 8.28995 ( 948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7651 (p90) cc_final: 0.7379 (p90) REVERT: A 60 LYS cc_start: 0.8832 (mmtt) cc_final: 0.7942 (mmtt) REVERT: A 164 GLU cc_start: 0.8178 (tt0) cc_final: 0.7932 (tt0) REVERT: H 105 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7374 (pp30) REVERT: E 44 GLU cc_start: 0.9150 (pm20) cc_final: 0.8933 (pm20) REVERT: E 209 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8296 (ttpp) outliers start: 9 outliers final: 1 residues processed: 107 average time/residue: 0.8716 time to fit residues: 97.5502 Evaluate side-chains 68 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 119 HIS A 173 HIS A 223 ASN F 210 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064921 restraints weight = 41907.214| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.82 r_work: 0.2932 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9026 Z= 0.178 Angle : 0.676 5.818 12347 Z= 0.360 Chirality : 0.045 0.161 1439 Planarity : 0.004 0.044 1578 Dihedral : 6.129 30.441 1279 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.49 % Allowed : 8.44 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1063 helix: -1.74 (0.60), residues: 51 sheet: 0.80 (0.25), residues: 407 loop : 0.05 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 177 TYR 0.015 0.002 TYR F 186 PHE 0.011 0.002 PHE A 41 TRP 0.021 0.001 TRP E 47 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9014) covalent geometry : angle 0.67530 (12323) SS BOND : bond 0.00462 ( 12) SS BOND : angle 0.88983 ( 24) hydrogen bonds : bond 0.04391 ( 346) hydrogen bonds : angle 5.88896 ( 948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 167 ASP cc_start: 0.8527 (t0) cc_final: 0.8195 (t0) REVERT: A 60 LYS cc_start: 0.8699 (mmtt) cc_final: 0.7923 (mmtp) REVERT: F 4 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7647 (mtp) REVERT: F 143 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: E 44 GLU cc_start: 0.9292 (pm20) cc_final: 0.9019 (pm20) REVERT: E 192 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7727 (tp-100) REVERT: E 209 LYS cc_start: 0.7419 (ttmm) cc_final: 0.7002 (ttpp) outliers start: 23 outliers final: 3 residues processed: 85 average time/residue: 0.8519 time to fit residues: 75.8183 Evaluate side-chains 73 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain E residue 62 TRP Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 21 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065249 restraints weight = 33322.434| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 4.32 r_work: 0.2952 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9026 Z= 0.163 Angle : 0.611 5.713 12347 Z= 0.323 Chirality : 0.044 0.171 1439 Planarity : 0.005 0.044 1578 Dihedral : 5.468 34.939 1276 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.95 % Allowed : 9.96 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1063 helix: -1.19 (0.66), residues: 51 sheet: 0.91 (0.25), residues: 432 loop : -0.03 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 177 TYR 0.016 0.001 TYR E 145 PHE 0.010 0.001 PHE A 41 TRP 0.019 0.001 TRP E 47 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9014) covalent geometry : angle 0.61060 (12323) SS BOND : bond 0.00364 ( 12) SS BOND : angle 0.75788 ( 24) hydrogen bonds : bond 0.03623 ( 346) hydrogen bonds : angle 5.34385 ( 948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7413 (tm-30) REVERT: A 109 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: A 163 MET cc_start: 0.8649 (mtp) cc_final: 0.8410 (mtm) REVERT: F 4 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7524 (mtp) REVERT: E 44 GLU cc_start: 0.9261 (pm20) cc_final: 0.8963 (pm20) REVERT: E 192 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7700 (tp-100) REVERT: E 206 LYS cc_start: 0.8332 (mppt) cc_final: 0.8062 (mppt) outliers start: 18 outliers final: 4 residues processed: 84 average time/residue: 0.8612 time to fit residues: 75.8018 Evaluate side-chains 74 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain E residue 62 TRP Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.090399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.064263 restraints weight = 48389.742| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 4.90 r_work: 0.2933 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9026 Z= 0.211 Angle : 0.631 5.857 12347 Z= 0.332 Chirality : 0.044 0.163 1439 Planarity : 0.005 0.046 1578 Dihedral : 5.439 33.134 1276 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.71 % Allowed : 10.93 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1063 helix: -0.95 (0.66), residues: 51 sheet: 0.76 (0.25), residues: 438 loop : -0.10 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 177 TYR 0.015 0.002 TYR F 49 PHE 0.013 0.002 PHE E 91 TRP 0.020 0.001 TRP E 47 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9014) covalent geometry : angle 0.63005 (12323) SS BOND : bond 0.00417 ( 12) SS BOND : angle 0.87893 ( 24) hydrogen bonds : bond 0.03616 ( 346) hydrogen bonds : angle 5.30123 ( 948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8104 (mmtp) REVERT: A 70 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 109 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7811 (mm-30) REVERT: H 105 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7263 (pp30) REVERT: F 4 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: F 143 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: E 5 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 44 GLU cc_start: 0.9326 (pm20) cc_final: 0.9115 (pm20) outliers start: 25 outliers final: 11 residues processed: 87 average time/residue: 0.8698 time to fit residues: 79.4204 Evaluate side-chains 82 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 161 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 TRP Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.065739 restraints weight = 41018.656| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.48 r_work: 0.2970 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9026 Z= 0.143 Angle : 0.584 6.230 12347 Z= 0.307 Chirality : 0.043 0.151 1439 Planarity : 0.005 0.047 1578 Dihedral : 5.160 32.017 1276 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.60 % Allowed : 11.90 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1063 helix: -0.72 (0.66), residues: 57 sheet: 0.83 (0.25), residues: 445 loop : -0.11 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 177 TYR 0.013 0.001 TYR H 194 PHE 0.009 0.001 PHE E 91 TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9014) covalent geometry : angle 0.58400 (12323) SS BOND : bond 0.00353 ( 12) SS BOND : angle 0.77509 ( 24) hydrogen bonds : bond 0.03291 ( 346) hydrogen bonds : angle 5.07624 ( 948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 143 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: L 195 GLU cc_start: 0.8442 (pm20) cc_final: 0.8120 (pm20) REVERT: A 60 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8132 (mmtp) REVERT: A 109 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7791 (mm-30) REVERT: A 174 ARG cc_start: 0.7892 (mmp80) cc_final: 0.7688 (mmp80) REVERT: F 4 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: F 143 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7999 (pp20) REVERT: E 43 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8744 (mttm) REVERT: E 44 GLU cc_start: 0.9252 (pm20) cc_final: 0.9038 (pm20) REVERT: E 192 GLN cc_start: 0.7910 (tp40) cc_final: 0.7580 (tp-100) REVERT: E 210 LYS cc_start: 0.9271 (tptp) cc_final: 0.9029 (tppp) outliers start: 24 outliers final: 9 residues processed: 84 average time/residue: 0.8778 time to fit residues: 77.3950 Evaluate side-chains 78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 62 TRP Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.090211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064254 restraints weight = 43976.998| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 4.66 r_work: 0.2942 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9026 Z= 0.202 Angle : 0.621 7.619 12347 Z= 0.324 Chirality : 0.044 0.148 1439 Planarity : 0.005 0.046 1578 Dihedral : 5.252 31.454 1276 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.71 % Allowed : 12.77 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1063 helix: -0.77 (0.65), residues: 57 sheet: 0.64 (0.25), residues: 456 loop : -0.18 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 177 TYR 0.016 0.002 TYR F 49 PHE 0.014 0.002 PHE E 91 TRP 0.019 0.001 TRP E 47 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 9014) covalent geometry : angle 0.62083 (12323) SS BOND : bond 0.00404 ( 12) SS BOND : angle 0.83400 ( 24) hydrogen bonds : bond 0.03480 ( 346) hydrogen bonds : angle 5.16470 ( 948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 145 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8706 (ttpp) REVERT: A 70 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7646 (tm-30) REVERT: A 109 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: F 4 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7573 (mtp) REVERT: F 143 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (pp20) REVERT: E 43 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8733 (mttm) REVERT: E 44 GLU cc_start: 0.9298 (pm20) cc_final: 0.9077 (pm20) REVERT: E 210 LYS cc_start: 0.9236 (tptp) cc_final: 0.8974 (tppp) outliers start: 25 outliers final: 13 residues processed: 85 average time/residue: 0.7943 time to fit residues: 71.0692 Evaluate side-chains 81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 62 TRP Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 67 optimal weight: 0.0170 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.092602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067235 restraints weight = 40909.756| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.45 r_work: 0.3013 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9026 Z= 0.104 Angle : 0.563 7.341 12347 Z= 0.293 Chirality : 0.042 0.136 1439 Planarity : 0.005 0.046 1578 Dihedral : 4.885 29.360 1276 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.62 % Allowed : 14.50 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 1063 helix: -0.43 (0.69), residues: 57 sheet: 0.82 (0.25), residues: 450 loop : -0.07 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 177 TYR 0.016 0.001 TYR H 194 PHE 0.008 0.001 PHE H 27 TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9014) covalent geometry : angle 0.56284 (12323) SS BOND : bond 0.00334 ( 12) SS BOND : angle 0.65546 ( 24) hydrogen bonds : bond 0.02936 ( 346) hydrogen bonds : angle 4.84484 ( 948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: L 145 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8744 (ttpp) REVERT: A 60 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8145 (mmtp) REVERT: A 70 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 109 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7729 (mm-30) REVERT: A 174 ARG cc_start: 0.7858 (mmp80) cc_final: 0.7632 (mmp80) REVERT: F 4 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: F 143 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8164 (pp20) REVERT: E 43 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8763 (mttm) REVERT: E 192 GLN cc_start: 0.7798 (tp40) cc_final: 0.7442 (tp-100) REVERT: E 206 LYS cc_start: 0.8436 (mppt) cc_final: 0.8001 (mppt) REVERT: E 210 LYS cc_start: 0.9189 (tptp) cc_final: 0.8977 (tppp) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 0.8915 time to fit residues: 77.4569 Evaluate side-chains 78 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.0270 chunk 101 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 83 optimal weight: 0.0270 chunk 65 optimal weight: 0.0570 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 192 GLN E 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068378 restraints weight = 50856.314| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.94 r_work: 0.3015 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9026 Z= 0.098 Angle : 0.555 7.208 12347 Z= 0.288 Chirality : 0.041 0.131 1439 Planarity : 0.005 0.046 1578 Dihedral : 4.674 28.906 1276 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.62 % Allowed : 15.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1063 helix: -0.33 (0.71), residues: 57 sheet: 0.90 (0.25), residues: 452 loop : -0.01 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 177 TYR 0.016 0.001 TYR H 194 PHE 0.008 0.001 PHE H 27 TRP 0.008 0.001 TRP A 38 HIS 0.003 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9014) covalent geometry : angle 0.55249 (12323) SS BOND : bond 0.00393 ( 12) SS BOND : angle 1.31028 ( 24) hydrogen bonds : bond 0.02809 ( 346) hydrogen bonds : angle 4.66614 ( 948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: L 145 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8696 (ttpp) REVERT: A 60 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8137 (mmtp) REVERT: A 70 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 109 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: A 156 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7902 (pttm) REVERT: A 174 ARG cc_start: 0.7837 (mmp80) cc_final: 0.7615 (mmp80) REVERT: F 4 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7779 (mtp) REVERT: F 143 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8193 (pp20) REVERT: E 43 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8722 (mttm) REVERT: E 192 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7453 (tp40) REVERT: E 206 LYS cc_start: 0.8419 (mppt) cc_final: 0.8002 (mppt) outliers start: 15 outliers final: 6 residues processed: 82 average time/residue: 0.8249 time to fit residues: 70.9671 Evaluate side-chains 77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.092600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066891 restraints weight = 46083.360| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.72 r_work: 0.2998 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9026 Z= 0.131 Angle : 0.569 7.334 12347 Z= 0.295 Chirality : 0.042 0.140 1439 Planarity : 0.005 0.046 1578 Dihedral : 4.709 28.489 1276 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.41 % Allowed : 15.37 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.27), residues: 1063 helix: -0.36 (0.70), residues: 58 sheet: 0.88 (0.25), residues: 451 loop : -0.03 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 177 TYR 0.015 0.001 TYR H 194 PHE 0.009 0.001 PHE E 91 TRP 0.012 0.001 TRP E 47 HIS 0.002 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9014) covalent geometry : angle 0.56711 (12323) SS BOND : bond 0.00382 ( 12) SS BOND : angle 1.21257 ( 24) hydrogen bonds : bond 0.03014 ( 346) hydrogen bonds : angle 4.68872 ( 948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8130 (mmtp) REVERT: A 70 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 109 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: A 156 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7862 (pttt) REVERT: A 174 ARG cc_start: 0.7823 (mmp80) cc_final: 0.7618 (mmp80) REVERT: F 4 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: E 43 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8757 (mttm) REVERT: E 206 LYS cc_start: 0.8409 (mppt) cc_final: 0.8007 (mppt) REVERT: E 210 LYS cc_start: 0.9229 (tptp) cc_final: 0.8998 (tppp) outliers start: 13 outliers final: 8 residues processed: 78 average time/residue: 0.8990 time to fit residues: 73.5275 Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 192 GLN ** F 198 HIS ** 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 = 0.3645 r_free = 0.3645 target = 0.091779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067104 restraints weight = 32713.981| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.99 r_work: 0.3017 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9026 Z= 0.159 Angle : 0.603 9.797 12347 Z= 0.313 Chirality : 0.042 0.142 1439 Planarity : 0.005 0.045 1578 Dihedral : 4.823 28.219 1276 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.52 % Allowed : 15.37 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1063 helix: -0.42 (0.69), residues: 58 sheet: 0.81 (0.26), residues: 438 loop : -0.03 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 188 TYR 0.013 0.001 TYR F 49 PHE 0.012 0.001 PHE E 91 TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS F 198 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9014) covalent geometry : angle 0.60127 (12323) SS BOND : bond 0.00389 ( 12) SS BOND : angle 1.24537 ( 24) hydrogen bonds : bond 0.03148 ( 346) hydrogen bonds : angle 4.81385 ( 948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7839 (p90) cc_final: 0.6256 (p90) REVERT: A 60 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8087 (mmtp) REVERT: A 70 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 109 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7740 (mm-30) REVERT: A 156 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7925 (pttt) REVERT: A 164 GLU cc_start: 0.7899 (tt0) cc_final: 0.7688 (tt0) REVERT: F 4 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7862 (mtp) REVERT: E 43 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8729 (mttm) REVERT: E 192 GLN cc_start: 0.7578 (tp40) cc_final: 0.7198 (tp-100) REVERT: E 206 LYS cc_start: 0.8420 (mppt) cc_final: 0.8026 (mppt) REVERT: E 210 LYS cc_start: 0.9173 (tptp) cc_final: 0.8944 (tppp) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.8381 time to fit residues: 69.5590 Evaluate side-chains 77 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 198 HIS ** 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 = 0.3652 r_free = 0.3652 target = 0.092142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066732 restraints weight = 43871.978| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 4.53 r_work: 0.2997 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9026 Z= 0.140 Angle : 0.591 10.180 12347 Z= 0.306 Chirality : 0.042 0.139 1439 Planarity : 0.005 0.045 1578 Dihedral : 4.801 27.283 1276 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.19 % Allowed : 15.69 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 1063 helix: -0.36 (0.70), residues: 58 sheet: 0.80 (0.26), residues: 438 loop : -0.03 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 188 TYR 0.012 0.001 TYR F 49 PHE 0.009 0.001 PHE E 91 TRP 0.014 0.001 TRP E 47 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9014) covalent geometry : angle 0.58958 (12323) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.15150 ( 24) hydrogen bonds : bond 0.03037 ( 346) hydrogen bonds : angle 4.78057 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3552.45 seconds wall clock time: 61 minutes 19.69 seconds (3679.69 seconds total)