Starting phenix.real_space_refine on Thu Mar 6 03:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.map" model { file = "/net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jps_36488/03_2025/8jps_36488.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.041 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 34 5.16 5 C 3034 2.51 5 N 751 2.21 5 O 797 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4616 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1890 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 427 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1884 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 415 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Time building chain proxies: 3.93, per 1000 atoms: 0.85 Number of scatterers: 4616 At special positions: 0 Unit cell: (132.383, 83.5612, 61.0279, 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 34 16.00 O 797 8.00 N 751 7.00 C 3034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 276 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 36 " distance=2.03 Simple disulfide: pdb=" SG CYS D 12 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 276 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS C 12 " - pdb=" SG CYS C 52 " 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: 1.24 Conformation dependent library (CDL) restraints added in 621.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 67.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 82 removed outlier: 4.345A pdb=" N THR B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.824A pdb=" N PHE B 88 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 89 " --> pdb=" O PRO B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 89' Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.624A pdb=" N LEU B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 125 through 158 removed outlier: 6.542A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 203 through 226 removed outlier: 4.483A pdb=" N LEU B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Proline residue: B 222 - end of helix Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 268 Proline residue: B 255 - end of helix removed outlier: 3.894A pdb=" N LEU B 260 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 295 Processing helix chain 'B' and resid 295 through 311 Proline residue: B 301 - end of helix Processing helix chain 'D' and resid 57 through 67 Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 82 removed outlier: 4.613A pdb=" N THR A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.692A pdb=" N PHE A 88 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.667A pdb=" N LEU A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 125 through 153 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 203 through 227 removed outlier: 4.398A pdb=" N LEU A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Proline residue: A 222 - end of helix Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.742A pdb=" N LEU A 260 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 295 Processing helix chain 'A' and resid 295 through 312 Proline residue: A 301 - end of helix removed outlier: 3.580A pdb=" N THR A 312 " --> pdb=" O CYS A 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.559A pdb=" N GLN C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.565A pdb=" N GLY B 189 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 25 through 29 removed outlier: 6.681A pdb=" N LYS D 44 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR D 28 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE D 42 " --> pdb=" O TYR D 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 191 removed outlier: 4.021A pdb=" N LEU A 194 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.812A pdb=" N VAL C 41 " --> pdb=" O ALA C 53 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 873 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: 1.19 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1418 1.34 - 1.46: 1082 1.46 - 1.58: 2194 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 4732 Sorted by residual: bond pdb=" N LYS D 18 " pdb=" CA LYS D 18 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.34e-02 5.57e+03 3.60e+00 bond pdb=" N TRP A 242 " pdb=" CA TRP A 242 " ideal model delta sigma weight residual 1.454 1.476 -0.022 1.17e-02 7.31e+03 3.50e+00 bond pdb=" N GLU B 46 " pdb=" CA GLU B 46 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.90e-02 2.77e+03 1.88e+00 bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.90e-02 2.77e+03 1.75e+00 bond pdb=" C LEU A 221 " pdb=" N PRO A 222 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.30e-02 5.92e+03 1.17e+00 ... (remaining 4727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 6160 1.33 - 2.67: 259 2.67 - 4.00: 48 4.00 - 5.33: 24 5.33 - 6.67: 7 Bond angle restraints: 6498 Sorted by residual: angle pdb=" N TRP A 242 " pdb=" CA TRP A 242 " pdb=" CB TRP A 242 " ideal model delta sigma weight residual 110.39 115.64 -5.25 1.59e+00 3.96e-01 1.09e+01 angle pdb=" C GLU B 46 " pdb=" N ALA B 47 " pdb=" CA ALA B 47 " ideal model delta sigma weight residual 120.88 115.74 5.14 1.62e+00 3.81e-01 1.01e+01 angle pdb=" CA LYS D 18 " pdb=" C LYS D 18 " pdb=" O LYS D 18 " ideal model delta sigma weight residual 121.87 118.23 3.64 1.16e+00 7.43e-01 9.87e+00 angle pdb=" O TRP A 242 " pdb=" C TRP A 242 " pdb=" N MET A 243 " ideal model delta sigma weight residual 121.83 125.84 -4.01 1.28e+00 6.10e-01 9.81e+00 angle pdb=" C ALA B 61 " pdb=" N LEU B 62 " pdb=" CA LEU B 62 " ideal model delta sigma weight residual 120.09 123.81 -3.72 1.25e+00 6.40e-01 8.87e+00 ... (remaining 6493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 2523 16.73 - 33.46: 166 33.46 - 50.19: 43 50.19 - 66.92: 7 66.92 - 83.65: 3 Dihedral angle restraints: 2742 sinusoidal: 910 harmonic: 1832 Sorted by residual: dihedral pdb=" CB CYS B 129 " pdb=" SG CYS B 129 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual 93.00 160.77 -67.77 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 276 " pdb=" CB CYS A 276 " ideal model delta sinusoidal sigma weight residual -86.00 -150.90 64.90 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA ASP B 58 " pdb=" C ASP B 58 " pdb=" N ASP B 59 " pdb=" CA ASP B 59 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 2739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 504 0.029 - 0.058: 193 0.058 - 0.087: 59 0.087 - 0.116: 49 0.116 - 0.145: 8 Chirality restraints: 813 Sorted by residual: chirality pdb=" CA THR B 300 " pdb=" N THR B 300 " pdb=" C THR B 300 " pdb=" CB THR B 300 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA GLU A 46 " pdb=" N GLU A 46 " pdb=" C GLU A 46 " pdb=" CB GLU A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA THR A 300 " pdb=" N THR A 300 " pdb=" C THR A 300 " pdb=" CB THR A 300 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 810 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 136 " -0.023 2.00e-02 2.50e+03 1.65e-02 6.85e+00 pdb=" CG TRP A 136 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 136 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 136 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 136 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 136 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 136 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 136 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 136 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 216 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ALA A 216 " 0.039 2.00e-02 2.50e+03 pdb=" O ALA A 216 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 217 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 216 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.95e+00 pdb=" C ALA B 216 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA B 216 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE B 217 " 0.013 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1431 2.83 - 3.35: 4786 3.35 - 3.86: 7403 3.86 - 4.38: 7931 4.38 - 4.90: 13694 Nonbonded interactions: 35245 Sorted by model distance: nonbonded pdb=" O SER A 53 " pdb=" ND2 ASN A 55 " model vdw 2.310 3.120 nonbonded pdb=" OE1 GLN A 143 " pdb=" NE1 TRP A 249 " model vdw 2.350 3.120 nonbonded pdb=" O SER B 122 " pdb=" OG1 THR B 123 " model vdw 2.356 3.040 nonbonded pdb=" O PHE B 264 " pdb=" OG SER B 268 " model vdw 2.361 3.040 nonbonded pdb=" O SER A 122 " pdb=" OG1 THR A 123 " model vdw 2.365 3.040 ... (remaining 35240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 46 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB )) or resid 180 through 242 or (resid 243 and (name N o \ r name CA or name C or name O or name CB )) or resid 244 through 312)) } ncs_group { reference = (chain 'C' and (resid 8 through 42 or (resid 43 through 44 and (name N or name C \ A or name C or name O or name CB )) or resid 45 through 46 or (resid 47 through \ 48 and (name N or name CA or name C or name O or name CB )) or resid 49 through \ 61 or (resid 62 through 66 and (name N or name CA or name C or name O or name CB \ )) or resid 67 through 70)) selection = (chain 'D' and (resid 8 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 22 or (resid 23 through 24 and (nam \ e N or name CA or name C or name O or name CB )) or resid 25 through 31 or (resi \ d 32 and (name N or name CA or name C or name O or name CB )) or resid 33 throug \ h 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or re \ sid 51 through 55 or (resid 56 through 59 and (name N or name CA or name C or na \ me O or name CB )) or resid 60 through 62 or (resid 63 through 66 and (name N or \ name CA or name C or name O or name CB )) or resid 67 through 70)) } 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: 1.790 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.150 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4732 Z= 0.201 Angle : 0.691 6.666 6498 Z= 0.380 Chirality : 0.041 0.145 813 Planarity : 0.004 0.035 791 Dihedral : 12.409 83.654 1530 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.43 % Allowed : 0.86 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.35), residues: 628 helix: 0.80 (0.29), residues: 364 sheet: 0.66 (1.16), residues: 24 loop : -1.96 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 136 HIS 0.004 0.001 HIS A 309 PHE 0.034 0.002 PHE B 109 TYR 0.007 0.002 TYR A 137 ARG 0.002 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: B 55 ASN cc_start: 0.5704 (t0) cc_final: 0.5482 (t0) REVERT: B 288 LEU cc_start: 0.7434 (tp) cc_final: 0.7096 (tt) REVERT: A 136 TRP cc_start: 0.7612 (t-100) cc_final: 0.7014 (t60) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1406 time to fit residues: 20.9670 Evaluate side-chains 92 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN D 23 GLN A 143 GLN A 150 HIS C 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124488 restraints weight = 10800.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.127522 restraints weight = 5956.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.129412 restraints weight = 3973.276| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4732 Z= 0.246 Angle : 0.671 7.137 6498 Z= 0.341 Chirality : 0.041 0.129 813 Planarity : 0.005 0.048 791 Dihedral : 4.893 20.361 654 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.37 % Allowed : 13.36 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.34), residues: 628 helix: 0.67 (0.29), residues: 366 sheet: 0.71 (1.13), residues: 24 loop : -2.00 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 136 HIS 0.004 0.001 HIS A 150 PHE 0.027 0.002 PHE B 81 TYR 0.012 0.002 TYR C 28 ARG 0.004 0.001 ARG B 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.510 Fit side-chains REVERT: B 55 ASN cc_start: 0.6105 (t0) cc_final: 0.5760 (t0) REVERT: B 254 TRP cc_start: 0.5824 (t-100) cc_final: 0.5575 (t-100) REVERT: B 288 LEU cc_start: 0.7432 (tp) cc_final: 0.7126 (tt) REVERT: A 112 VAL cc_start: 0.8095 (p) cc_final: 0.7792 (t) outliers start: 11 outliers final: 6 residues processed: 95 average time/residue: 0.1209 time to fit residues: 15.7938 Evaluate side-chains 96 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 GLN D 23 GLN A 279 GLN C 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.142607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.125782 restraints weight = 10909.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.128817 restraints weight = 5974.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.130689 restraints weight = 3974.072| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4732 Z= 0.197 Angle : 0.649 8.202 6498 Z= 0.327 Chirality : 0.041 0.289 813 Planarity : 0.005 0.045 791 Dihedral : 4.739 19.011 654 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.72 % Allowed : 17.89 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.34), residues: 628 helix: 0.59 (0.28), residues: 376 sheet: 0.32 (1.07), residues: 24 loop : -2.00 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 136 HIS 0.002 0.001 HIS A 256 PHE 0.022 0.002 PHE B 81 TYR 0.008 0.001 TYR D 13 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.477 Fit side-chains REVERT: B 288 LEU cc_start: 0.7443 (tp) cc_final: 0.7145 (tt) outliers start: 8 outliers final: 5 residues processed: 97 average time/residue: 0.1155 time to fit residues: 15.5326 Evaluate side-chains 98 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN A 143 GLN C 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.122355 restraints weight = 11341.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124694 restraints weight = 7001.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.126135 restraints weight = 5140.149| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4732 Z= 0.272 Angle : 0.678 7.785 6498 Z= 0.339 Chirality : 0.042 0.154 813 Planarity : 0.005 0.045 791 Dihedral : 4.801 18.863 654 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.45 % Allowed : 19.61 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.34), residues: 628 helix: 0.58 (0.28), residues: 370 sheet: -0.13 (1.05), residues: 24 loop : -2.06 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 136 HIS 0.007 0.001 HIS B 296 PHE 0.024 0.002 PHE B 81 TYR 0.012 0.002 TYR C 28 ARG 0.002 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.475 Fit side-chains REVERT: B 146 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 147 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6680 (mm) REVERT: B 288 LEU cc_start: 0.7547 (tp) cc_final: 0.7227 (tt) REVERT: D 23 GLN cc_start: 0.8399 (tp40) cc_final: 0.8181 (tp-100) REVERT: A 221 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6624 (tt) outliers start: 16 outliers final: 8 residues processed: 98 average time/residue: 0.1021 time to fit residues: 14.3113 Evaluate side-chains 101 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN C 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.122883 restraints weight = 11040.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.125606 restraints weight = 6350.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127367 restraints weight = 4394.890| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4732 Z= 0.242 Angle : 0.669 6.807 6498 Z= 0.335 Chirality : 0.041 0.145 813 Planarity : 0.005 0.044 791 Dihedral : 4.773 18.617 654 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.45 % Allowed : 20.91 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.34), residues: 628 helix: 0.56 (0.28), residues: 370 sheet: -0.49 (1.03), residues: 24 loop : -2.00 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 136 HIS 0.004 0.001 HIS B 296 PHE 0.021 0.002 PHE B 81 TYR 0.006 0.001 TYR A 199 ARG 0.002 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: B 146 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7899 (mp) REVERT: B 179 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 288 LEU cc_start: 0.7516 (tp) cc_final: 0.7203 (tt) REVERT: A 147 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6647 (mm) REVERT: A 221 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6684 (tt) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1055 time to fit residues: 15.3289 Evaluate side-chains 106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.140782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.123645 restraints weight = 10817.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.126538 restraints weight = 6083.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.128370 restraints weight = 4146.588| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4732 Z= 0.215 Angle : 0.656 7.577 6498 Z= 0.328 Chirality : 0.041 0.146 813 Planarity : 0.005 0.044 791 Dihedral : 4.640 18.007 654 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.23 % Allowed : 21.34 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.34), residues: 628 helix: 0.64 (0.28), residues: 370 sheet: -1.30 (0.89), residues: 34 loop : -1.89 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 136 HIS 0.004 0.001 HIS B 296 PHE 0.027 0.002 PHE A 264 TYR 0.011 0.001 TYR C 28 ARG 0.001 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.488 Fit side-chains REVERT: B 146 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7905 (mp) REVERT: B 147 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6495 (mm) REVERT: B 288 LEU cc_start: 0.7497 (tp) cc_final: 0.7152 (tt) REVERT: A 147 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6615 (mm) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.1252 time to fit residues: 17.4460 Evaluate side-chains 106 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.140330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.123648 restraints weight = 10869.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.126591 restraints weight = 6066.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.128458 restraints weight = 4104.173| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4732 Z= 0.244 Angle : 0.715 13.205 6498 Z= 0.352 Chirality : 0.042 0.142 813 Planarity : 0.005 0.044 791 Dihedral : 4.687 17.619 654 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.09 % Allowed : 21.77 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.34), residues: 628 helix: 0.63 (0.28), residues: 370 sheet: -1.34 (0.91), residues: 34 loop : -1.88 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.002 PHE A 264 TYR 0.007 0.001 TYR A 199 ARG 0.001 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.483 Fit side-chains REVERT: B 146 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 147 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6407 (mm) REVERT: B 288 LEU cc_start: 0.7504 (tp) cc_final: 0.7301 (tp) REVERT: A 147 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6679 (mm) REVERT: A 221 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6649 (tt) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.1016 time to fit residues: 14.3016 Evaluate side-chains 102 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.138717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.122300 restraints weight = 11292.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.124801 restraints weight = 6883.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126362 restraints weight = 4975.289| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4732 Z= 0.280 Angle : 0.731 12.729 6498 Z= 0.359 Chirality : 0.043 0.138 813 Planarity : 0.005 0.044 791 Dihedral : 4.737 17.642 654 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.31 % Allowed : 22.84 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.34), residues: 628 helix: 0.60 (0.28), residues: 366 sheet: -1.43 (0.92), residues: 34 loop : -1.97 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.031 0.002 PHE A 264 TYR 0.011 0.002 TYR C 28 ARG 0.002 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.469 Fit side-chains REVERT: B 146 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7827 (mp) REVERT: B 147 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6489 (mm) REVERT: B 288 LEU cc_start: 0.7511 (tp) cc_final: 0.7189 (tt) REVERT: D 23 GLN cc_start: 0.8380 (tp40) cc_final: 0.8155 (tp-100) REVERT: A 147 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6774 (mm) REVERT: A 221 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6585 (tt) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.1129 time to fit residues: 15.2750 Evaluate side-chains 104 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 6 optimal weight: 0.2980 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.141083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.124247 restraints weight = 10968.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.127229 restraints weight = 6032.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.129111 restraints weight = 4052.849| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4732 Z= 0.217 Angle : 0.711 11.641 6498 Z= 0.349 Chirality : 0.041 0.141 813 Planarity : 0.005 0.043 791 Dihedral : 4.621 17.222 654 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.74 % Allowed : 22.63 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.34), residues: 628 helix: 0.66 (0.28), residues: 370 sheet: -1.46 (0.92), residues: 34 loop : -1.81 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.001 PHE A 264 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.402 Fit side-chains REVERT: B 146 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 147 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6433 (mm) REVERT: D 23 GLN cc_start: 0.8487 (tp40) cc_final: 0.8277 (tp-100) REVERT: A 147 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6632 (mm) REVERT: A 221 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6584 (tt) outliers start: 22 outliers final: 13 residues processed: 104 average time/residue: 0.1144 time to fit residues: 16.4157 Evaluate side-chains 105 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.121887 restraints weight = 11051.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.124828 restraints weight = 6221.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.126680 restraints weight = 4243.404| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4732 Z= 0.257 Angle : 0.740 11.827 6498 Z= 0.360 Chirality : 0.042 0.138 813 Planarity : 0.005 0.044 791 Dihedral : 4.673 17.134 654 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.45 % Allowed : 23.92 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.34), residues: 628 helix: 0.66 (0.28), residues: 366 sheet: -1.56 (0.92), residues: 34 loop : -1.90 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.036 0.002 PHE A 264 TYR 0.020 0.002 TYR C 28 ARG 0.002 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.491 Fit side-chains REVERT: B 146 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7902 (mp) REVERT: B 147 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6455 (mm) REVERT: A 147 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6664 (mm) REVERT: A 221 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6577 (tt) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.1193 time to fit residues: 15.8155 Evaluate side-chains 100 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN A 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.139692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.122374 restraints weight = 11133.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.125369 restraints weight = 6277.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127287 restraints weight = 4269.339| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4732 Z= 0.242 Angle : 0.751 11.277 6498 Z= 0.365 Chirality : 0.042 0.210 813 Planarity : 0.005 0.043 791 Dihedral : 4.655 17.314 654 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.45 % Allowed : 24.78 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.34), residues: 628 helix: 0.68 (0.28), residues: 366 sheet: -1.53 (0.91), residues: 34 loop : -1.88 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 136 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.001 PHE A 264 TYR 0.008 0.001 TYR A 199 ARG 0.001 0.000 ARG B 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1648.08 seconds wall clock time: 29 minutes 28.02 seconds (1768.02 seconds total)