Starting phenix.real_space_refine on Fri Dec 27 14:30:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.cif Found real_map, /net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.map" model { file = "/net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7etw_31303/12_2024/7etw_31303.cif" } resolution = 4.1 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= 0.000 sd= 0.005 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 20 5.16 5 C 3204 2.51 5 N 784 2.21 5 O 944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4952 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1525 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 188} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3059 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 25, 'TRANS': 457} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1104 Unresolved non-hydrogen dihedrals: 724 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 11, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 6, 'ASP:plan': 10, 'PHE:plan': 10, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 456 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 340 Unusual residues: {'AJP': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.75, per 1000 atoms: 0.76 Number of scatterers: 4952 At special positions: 0 Unit cell: (85.098, 86.189, 123.283, 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 20 16.00 O 944 8.00 N 784 7.00 C 3204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN B 641 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 813.7 milliseconds 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1274 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 64.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 18 through 48 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 72 through 95 removed outlier: 4.008A pdb=" N CYS A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.812A pdb=" N ASP A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 121 removed outlier: 3.791A pdb=" N VAL A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.525A pdb=" N LEU A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 173 removed outlier: 3.575A pdb=" N GLY A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 191 removed outlier: 4.007A pdb=" N ARG A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 212 removed outlier: 3.584A pdb=" N ILE A 195 " --> pdb=" O TRP A 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.605A pdb=" N PHE B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 41 removed outlier: 3.811A pdb=" N ILE B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 131 removed outlier: 3.626A pdb=" N SER B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Proline residue: B 118 - end of helix removed outlier: 3.951A pdb=" N GLN B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.501A pdb=" N GLU B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 removed outlier: 3.705A pdb=" N ARG B 158 " --> pdb=" O PRO B 155 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 159 " --> pdb=" O GLY B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 191 through 197 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 244 through 259 removed outlier: 3.605A pdb=" N LEU B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 285 through 305 removed outlier: 3.716A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 4.364A pdb=" N ALA B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 removed outlier: 3.598A pdb=" N LEU B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 5.421A pdb=" N LEU B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 367 " --> pdb=" O VAL B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 removed outlier: 3.854A pdb=" N ARG B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 433 removed outlier: 4.607A pdb=" N LEU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 3.719A pdb=" N THR B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 533 Processing helix chain 'B' and resid 534 through 538 Processing helix chain 'B' and resid 632 through 639 removed outlier: 3.996A pdb=" N LEU B 636 " --> pdb=" O HIS B 632 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.805A pdb=" N VAL B 232 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 98 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 654 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 97 " --> pdb=" O VAL B 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.805A pdb=" N VAL B 232 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL B 98 " --> pdb=" O TYR B 234 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N THR B 658 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS B 99 " --> pdb=" O THR B 658 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.882A pdb=" N LEU B 134 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 272 through 275 removed outlier: 4.460A pdb=" N VAL B 272 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 651 " --> pdb=" O VAL B 272 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 852 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: 1.37 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 747 1.32 - 1.44: 1388 1.44 - 1.56: 2907 1.56 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 5072 Sorted by residual: bond pdb=" C LYS B 277 " pdb=" O LYS B 277 " ideal model delta sigma weight residual 1.235 1.281 -0.047 1.18e-02 7.18e+03 1.57e+01 bond pdb=" N ARG B 660 " pdb=" CA ARG B 660 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.18e-02 7.18e+03 1.55e+01 bond pdb=" N VAL B 654 " pdb=" CA VAL B 654 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.14e-02 7.69e+03 1.45e+01 bond pdb=" N VAL B 657 " pdb=" CA VAL B 657 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N LYS B 99 " pdb=" CA LYS B 99 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.24e-02 6.50e+03 1.30e+01 ... (remaining 5067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 6455 2.09 - 4.18: 479 4.18 - 6.27: 73 6.27 - 8.36: 12 8.36 - 10.45: 5 Bond angle restraints: 7024 Sorted by residual: angle pdb=" N PRO B 104 " pdb=" CA PRO B 104 " pdb=" C PRO B 104 " ideal model delta sigma weight residual 113.84 104.13 9.71 1.30e+00 5.92e-01 5.58e+01 angle pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 106.32 116.68 -10.36 1.61e+00 3.86e-01 4.14e+01 angle pdb=" CA SER B 173 " pdb=" C SER B 173 " pdb=" N PRO B 174 " ideal model delta sigma weight residual 117.95 122.09 -4.14 7.70e-01 1.69e+00 2.90e+01 angle pdb=" C ARG B 267 " pdb=" CA ARG B 267 " pdb=" CB ARG B 267 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" C PRO B 89 " pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 122.48 128.15 -5.67 1.25e+00 6.40e-01 2.05e+01 ... (remaining 7019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.75: 3423 22.75 - 45.51: 171 45.51 - 68.26: 26 68.26 - 91.02: 6 91.02 - 113.77: 2 Dihedral angle restraints: 3628 sinusoidal: 1663 harmonic: 1965 Sorted by residual: dihedral pdb=" C ILE A 51 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" CB ILE A 51 " ideal model delta harmonic sigma weight residual -122.00 -133.18 11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" CA LYS A 102 " pdb=" C LYS A 102 " pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta harmonic sigma weight residual 180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA VAL A 55 " pdb=" C VAL A 55 " pdb=" N THR A 56 " pdb=" CA THR A 56 " ideal model delta harmonic sigma weight residual 180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 958 0.254 - 0.509: 5 0.509 - 0.763: 0 0.763 - 1.018: 0 1.018 - 1.272: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.13 -1.27 2.00e-02 2.50e+03 4.04e+03 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C11 AJP A 302 " pdb=" C10 AJP A 302 " pdb=" C12 AJP A 302 " pdb=" C16 AJP A 302 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 961 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.157 2.00e-02 2.50e+03 1.35e-01 2.27e+02 pdb=" C7 NAG D 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.029 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 641 " 0.093 2.00e-02 2.50e+03 1.35e-01 2.26e+02 pdb=" CG ASN B 641 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 641 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN B 641 " -0.238 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.113 2.00e-02 2.50e+03 9.24e-02 1.07e+02 pdb=" C7 NAG D 1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.084 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 29 2.45 - 3.07: 4058 3.07 - 3.68: 6953 3.68 - 4.29: 9646 4.29 - 4.90: 14668 Nonbonded interactions: 35354 Sorted by model distance: nonbonded pdb=" O53 AJP A 302 " pdb=" O76 AJP A 302 " model vdw 1.843 3.040 nonbonded pdb=" O43 AJP A 304 " pdb=" O50 AJP A 304 " model vdw 2.094 3.040 nonbonded pdb=" O60 AJP A 303 " pdb=" O77 AJP A 303 " model vdw 2.245 3.040 nonbonded pdb=" O ILE B 280 " pdb=" O GLY B 281 " model vdw 2.262 3.040 nonbonded pdb=" O ALA B 382 " pdb=" OG SER B 386 " model vdw 2.268 3.040 ... (remaining 35349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.480 Find NCS groups from input model: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.009 0.055 5072 Z= 0.617 Angle : 1.207 10.452 7024 Z= 0.682 Chirality : 0.076 1.272 964 Planarity : 0.008 0.135 812 Dihedral : 13.698 113.769 2354 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.64 % Favored : 86.42 % Rotamer: Outliers : 1.36 % Allowed : 4.90 % Favored : 93.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.24), residues: 670 helix: -3.25 (0.19), residues: 375 sheet: -1.07 (1.06), residues: 26 loop : -4.37 (0.28), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 633 HIS 0.024 0.004 HIS B 632 PHE 0.013 0.002 PHE A 155 TYR 0.027 0.002 TYR A 88 ARG 0.005 0.001 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6893 (tmt170) REVERT: A 167 VAL cc_start: 0.9082 (t) cc_final: 0.8821 (p) REVERT: A 208 ARG cc_start: 0.8669 (mtt180) cc_final: 0.7914 (mtt180) REVERT: A 209 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7542 (tp-100) REVERT: B 359 GLU cc_start: 0.7777 (mp0) cc_final: 0.7517 (mp0) REVERT: B 378 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8018 (ttmm) REVERT: B 383 GLN cc_start: 0.9147 (tt0) cc_final: 0.8482 (mt0) REVERT: B 388 GLU cc_start: 0.8434 (tp30) cc_final: 0.7911 (tp30) REVERT: B 442 ILE cc_start: 0.8824 (tp) cc_final: 0.8532 (mm) REVERT: B 445 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8018 (mmm160) REVERT: B 447 MET cc_start: 0.7903 (ttt) cc_final: 0.7536 (ttm) REVERT: B 626 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7315 (mmp80) REVERT: B 627 LYS cc_start: 0.7899 (mttt) cc_final: 0.7563 (pttm) REVERT: B 641 ASN cc_start: 0.6111 (t0) cc_final: 0.5609 (t0) outliers start: 5 outliers final: 1 residues processed: 160 average time/residue: 0.2015 time to fit residues: 39.5815 Evaluate side-chains 106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS B 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5072 Z= 0.274 Angle : 0.832 7.688 7024 Z= 0.397 Chirality : 0.047 0.361 964 Planarity : 0.006 0.088 812 Dihedral : 9.305 67.972 1629 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.72 % Favored : 92.54 % Rotamer: Outliers : 0.27 % Allowed : 8.45 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.30), residues: 670 helix: -0.95 (0.24), residues: 391 sheet: -1.33 (0.85), residues: 39 loop : -3.30 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 146 HIS 0.011 0.002 HIS B 632 PHE 0.022 0.002 PHE B 301 TYR 0.023 0.002 TYR A 88 ARG 0.007 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7201 (ptp-170) REVERT: A 209 GLN cc_start: 0.8557 (tp-100) cc_final: 0.7923 (tp-100) REVERT: B 298 TYR cc_start: 0.8624 (t80) cc_final: 0.8139 (t80) REVERT: B 347 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 378 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8133 (ttmm) REVERT: B 380 ARG cc_start: 0.8479 (ttt90) cc_final: 0.8199 (ttt180) REVERT: B 383 GLN cc_start: 0.9101 (tt0) cc_final: 0.8573 (mt0) REVERT: B 388 GLU cc_start: 0.8519 (tp30) cc_final: 0.8252 (tp30) REVERT: B 442 ILE cc_start: 0.8856 (tp) cc_final: 0.8577 (mm) REVERT: B 445 ARG cc_start: 0.8371 (ttt90) cc_final: 0.7887 (mmm160) REVERT: B 627 LYS cc_start: 0.7901 (mttt) cc_final: 0.7630 (pttm) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1857 time to fit residues: 32.9379 Evaluate side-chains 105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 120 HIS B 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5072 Z= 0.214 Angle : 0.724 8.063 7024 Z= 0.343 Chirality : 0.043 0.333 964 Planarity : 0.005 0.081 812 Dihedral : 8.355 65.403 1629 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.37 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.33), residues: 670 helix: 0.24 (0.26), residues: 388 sheet: -0.55 (0.91), residues: 37 loop : -2.83 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 146 HIS 0.021 0.003 HIS B 632 PHE 0.023 0.002 PHE B 420 TYR 0.021 0.002 TYR A 178 ARG 0.004 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7683 (mtm-85) cc_final: 0.7367 (ptp-170) REVERT: A 132 GLN cc_start: 0.6342 (mm110) cc_final: 0.5993 (mm110) REVERT: A 166 THR cc_start: 0.9250 (m) cc_final: 0.8730 (m) REVERT: A 170 GLN cc_start: 0.8627 (pm20) cc_final: 0.7878 (pm20) REVERT: A 209 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8220 (tp-100) REVERT: B 40 CYS cc_start: 0.6046 (m) cc_final: 0.5832 (m) REVERT: B 298 TYR cc_start: 0.8775 (t80) cc_final: 0.8031 (t80) REVERT: B 329 MET cc_start: 0.8261 (mtp) cc_final: 0.7989 (mtm) REVERT: B 347 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 359 GLU cc_start: 0.7854 (mp0) cc_final: 0.7638 (mp0) REVERT: B 378 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8159 (ttmm) REVERT: B 383 GLN cc_start: 0.9111 (tt0) cc_final: 0.8631 (mt0) REVERT: B 388 GLU cc_start: 0.8707 (tp30) cc_final: 0.8394 (tp30) REVERT: B 442 ILE cc_start: 0.8847 (tp) cc_final: 0.8577 (mm) REVERT: B 445 ARG cc_start: 0.8269 (ttt90) cc_final: 0.7684 (mmm160) REVERT: B 627 LYS cc_start: 0.7890 (mttt) cc_final: 0.7646 (pttm) REVERT: B 641 ASN cc_start: 0.4953 (t0) cc_final: 0.4725 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1686 time to fit residues: 27.6126 Evaluate side-chains 109 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 50.0000 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.0470 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5072 Z= 0.210 Angle : 0.690 6.916 7024 Z= 0.332 Chirality : 0.043 0.324 964 Planarity : 0.004 0.045 812 Dihedral : 7.885 63.273 1629 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.42 % Favored : 92.99 % Rotamer: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % 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: -0.97 (0.33), residues: 670 helix: 0.49 (0.26), residues: 389 sheet: -0.48 (0.92), residues: 37 loop : -2.58 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 146 HIS 0.007 0.002 HIS B 632 PHE 0.013 0.002 PHE B 435 TYR 0.011 0.001 TYR B 639 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7555 (ptp-170) REVERT: A 92 ASP cc_start: 0.7832 (t0) cc_final: 0.7567 (t0) REVERT: A 103 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7884 (tpp80) REVERT: A 132 GLN cc_start: 0.6340 (mm110) cc_final: 0.5940 (mm110) REVERT: A 209 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8269 (tp-100) REVERT: B 16 TYR cc_start: 0.8465 (t80) cc_final: 0.7855 (t80) REVERT: B 298 TYR cc_start: 0.8947 (t80) cc_final: 0.8582 (t80) REVERT: B 347 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 359 GLU cc_start: 0.7902 (mp0) cc_final: 0.7635 (mp0) REVERT: B 378 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8166 (ttmm) REVERT: B 383 GLN cc_start: 0.9143 (tt0) cc_final: 0.8720 (mt0) REVERT: B 388 GLU cc_start: 0.8777 (tp30) cc_final: 0.8541 (mm-30) REVERT: B 396 MET cc_start: 0.7244 (ttm) cc_final: 0.6943 (ttm) REVERT: B 442 ILE cc_start: 0.8871 (tp) cc_final: 0.8643 (mm) REVERT: B 627 LYS cc_start: 0.7888 (mttt) cc_final: 0.7651 (pttm) REVERT: B 641 ASN cc_start: 0.5081 (t0) cc_final: 0.4873 (t0) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.1719 time to fit residues: 29.9597 Evaluate side-chains 110 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 55 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5072 Z= 0.167 Angle : 0.662 9.359 7024 Z= 0.316 Chirality : 0.041 0.306 964 Planarity : 0.004 0.039 812 Dihedral : 7.555 61.469 1629 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.07 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.34), residues: 670 helix: 0.79 (0.27), residues: 392 sheet: -0.39 (0.92), residues: 37 loop : -2.51 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 146 HIS 0.007 0.002 HIS B 632 PHE 0.017 0.001 PHE B 436 TYR 0.009 0.001 TYR A 178 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7540 (ptp-170) REVERT: A 92 ASP cc_start: 0.7868 (t0) cc_final: 0.7625 (t0) REVERT: A 132 GLN cc_start: 0.6379 (mm110) cc_final: 0.5838 (mm110) REVERT: A 149 ASP cc_start: 0.8918 (t0) cc_final: 0.8611 (t70) REVERT: A 209 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8293 (tp-100) REVERT: B 16 TYR cc_start: 0.8477 (t80) cc_final: 0.7821 (t80) REVERT: B 298 TYR cc_start: 0.8961 (t80) cc_final: 0.8542 (t80) REVERT: B 347 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 359 GLU cc_start: 0.7918 (mp0) cc_final: 0.7714 (mp0) REVERT: B 362 LEU cc_start: 0.8661 (mt) cc_final: 0.8016 (tt) REVERT: B 383 GLN cc_start: 0.9150 (tt0) cc_final: 0.8734 (mt0) REVERT: B 396 MET cc_start: 0.7372 (ttm) cc_final: 0.7049 (ttm) REVERT: B 442 ILE cc_start: 0.8873 (tp) cc_final: 0.8642 (mm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1915 time to fit residues: 32.9512 Evaluate side-chains 110 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.0070 chunk 53 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5072 Z= 0.204 Angle : 0.672 6.472 7024 Z= 0.327 Chirality : 0.043 0.301 964 Planarity : 0.004 0.037 812 Dihedral : 7.463 60.130 1629 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.42 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.34), residues: 670 helix: 0.92 (0.27), residues: 390 sheet: -0.44 (0.93), residues: 37 loop : -2.39 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 146 HIS 0.003 0.001 HIS B 18 PHE 0.015 0.002 PHE A 197 TYR 0.020 0.002 TYR A 180 ARG 0.001 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7869 (mtm-85) cc_final: 0.7576 (ptp-170) REVERT: A 120 HIS cc_start: 0.8536 (t-90) cc_final: 0.8283 (t-170) REVERT: A 132 GLN cc_start: 0.6256 (mm110) cc_final: 0.5729 (mm110) REVERT: A 164 LEU cc_start: 0.7604 (mm) cc_final: 0.6887 (tt) REVERT: A 166 THR cc_start: 0.9225 (m) cc_final: 0.8733 (m) REVERT: A 170 GLN cc_start: 0.8456 (pm20) cc_final: 0.7572 (pm20) REVERT: B 16 TYR cc_start: 0.8445 (t80) cc_final: 0.8055 (t80) REVERT: B 298 TYR cc_start: 0.9030 (t80) cc_final: 0.8587 (t80) REVERT: B 347 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7003 (tp30) REVERT: B 359 GLU cc_start: 0.7881 (mp0) cc_final: 0.7622 (mp0) REVERT: B 362 LEU cc_start: 0.8648 (mt) cc_final: 0.8008 (tt) REVERT: B 378 LYS cc_start: 0.8932 (mtpp) cc_final: 0.8720 (mtpp) REVERT: B 383 GLN cc_start: 0.9134 (tt0) cc_final: 0.8782 (mt0) REVERT: B 442 ILE cc_start: 0.8892 (tp) cc_final: 0.8656 (mm) REVERT: B 630 PHE cc_start: 0.7866 (t80) cc_final: 0.7311 (m-80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1749 time to fit residues: 30.2252 Evaluate side-chains 110 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 chunk 29 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 40.0000 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 40.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 5072 Z= 0.515 Angle : 0.946 11.262 7024 Z= 0.456 Chirality : 0.052 0.406 964 Planarity : 0.005 0.039 812 Dihedral : 8.586 60.382 1629 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.96 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.32), residues: 670 helix: 0.18 (0.25), residues: 405 sheet: -0.88 (0.88), residues: 39 loop : -2.63 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 146 HIS 0.006 0.001 HIS A 120 PHE 0.022 0.003 PHE A 196 TYR 0.019 0.003 TYR B 292 ARG 0.003 0.001 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6488 (mmm) cc_final: 0.6217 (mmm) REVERT: A 31 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7792 (ptp-170) REVERT: A 103 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8214 (tpp80) REVERT: A 132 GLN cc_start: 0.6669 (mm110) cc_final: 0.6092 (mm110) REVERT: A 170 GLN cc_start: 0.8592 (pm20) cc_final: 0.8014 (pm20) REVERT: A 186 LEU cc_start: 0.9178 (tp) cc_final: 0.8938 (tp) REVERT: A 190 SER cc_start: 0.8859 (p) cc_final: 0.8402 (p) REVERT: B 16 TYR cc_start: 0.8668 (t80) cc_final: 0.8280 (t80) REVERT: B 359 GLU cc_start: 0.8065 (mp0) cc_final: 0.7689 (mp0) REVERT: B 362 LEU cc_start: 0.8742 (mt) cc_final: 0.8102 (tt) REVERT: B 383 GLN cc_start: 0.9193 (tt0) cc_final: 0.8822 (mt0) REVERT: B 415 GLN cc_start: 0.8266 (mt0) cc_final: 0.7080 (mt0) REVERT: B 442 ILE cc_start: 0.9017 (tp) cc_final: 0.8778 (mm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1778 time to fit residues: 29.1301 Evaluate side-chains 105 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 36 optimal weight: 0.0270 chunk 26 optimal weight: 0.0020 chunk 47 optimal weight: 3.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5072 Z= 0.192 Angle : 0.735 7.054 7024 Z= 0.352 Chirality : 0.044 0.331 964 Planarity : 0.004 0.040 812 Dihedral : 7.731 58.751 1629 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.82 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.33), residues: 670 helix: 0.74 (0.26), residues: 393 sheet: -0.54 (0.92), residues: 39 loop : -2.30 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 146 HIS 0.006 0.002 HIS A 99 PHE 0.023 0.002 PHE B 436 TYR 0.023 0.002 TYR B 639 ARG 0.002 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7643 (m) cc_final: 0.7333 (p) REVERT: A 31 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7665 (ptp-170) REVERT: A 103 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7825 (mmt90) REVERT: A 104 GLU cc_start: 0.8233 (tp30) cc_final: 0.7804 (pt0) REVERT: A 132 GLN cc_start: 0.6483 (mm110) cc_final: 0.5895 (mm110) REVERT: A 166 THR cc_start: 0.9240 (m) cc_final: 0.8953 (m) REVERT: A 170 GLN cc_start: 0.8475 (pm20) cc_final: 0.7821 (pm20) REVERT: A 191 TRP cc_start: 0.8815 (t-100) cc_final: 0.8459 (t-100) REVERT: A 209 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8307 (tp-100) REVERT: B 16 TYR cc_start: 0.8513 (t80) cc_final: 0.8125 (t80) REVERT: B 300 TYR cc_start: 0.8540 (t80) cc_final: 0.8184 (t80) REVERT: B 304 ARG cc_start: 0.8126 (tpt90) cc_final: 0.7813 (tpp80) REVERT: B 329 MET cc_start: 0.8140 (mtm) cc_final: 0.7835 (mmp) REVERT: B 347 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 359 GLU cc_start: 0.7950 (mp0) cc_final: 0.7697 (mp0) REVERT: B 362 LEU cc_start: 0.8600 (mt) cc_final: 0.7977 (tt) REVERT: B 378 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8385 (tppt) REVERT: B 383 GLN cc_start: 0.9140 (tt0) cc_final: 0.8800 (mt0) REVERT: B 415 GLN cc_start: 0.7895 (mt0) cc_final: 0.6512 (mt0) REVERT: B 430 PHE cc_start: 0.7094 (t80) cc_final: 0.6867 (t80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1722 time to fit residues: 30.8341 Evaluate side-chains 112 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 38 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5072 Z= 0.248 Angle : 0.732 8.562 7024 Z= 0.356 Chirality : 0.045 0.346 964 Planarity : 0.004 0.036 812 Dihedral : 7.629 58.576 1629 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.31 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 670 helix: 0.76 (0.26), residues: 396 sheet: -0.61 (0.91), residues: 39 loop : -2.22 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 146 HIS 0.002 0.001 HIS A 120 PHE 0.022 0.002 PHE B 436 TYR 0.021 0.001 TYR A 88 ARG 0.003 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7664 (m) cc_final: 0.7360 (p) REVERT: A 31 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7791 (ptp-170) REVERT: A 103 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7671 (mmt90) REVERT: A 132 GLN cc_start: 0.6572 (mm110) cc_final: 0.5963 (mm110) REVERT: A 166 THR cc_start: 0.9249 (m) cc_final: 0.8923 (m) REVERT: A 170 GLN cc_start: 0.8475 (pm20) cc_final: 0.7749 (pm20) REVERT: A 190 SER cc_start: 0.8836 (p) cc_final: 0.8528 (p) REVERT: A 209 GLN cc_start: 0.8960 (tp-100) cc_final: 0.8175 (tp-100) REVERT: B 16 TYR cc_start: 0.8609 (t80) cc_final: 0.8213 (t80) REVERT: B 300 TYR cc_start: 0.8618 (t80) cc_final: 0.8331 (t80) REVERT: B 304 ARG cc_start: 0.8183 (tpt90) cc_final: 0.7853 (tpp80) REVERT: B 329 MET cc_start: 0.8063 (mtm) cc_final: 0.7708 (mmp) REVERT: B 347 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7024 (tp30) REVERT: B 359 GLU cc_start: 0.7991 (mp0) cc_final: 0.7667 (mp0) REVERT: B 362 LEU cc_start: 0.8571 (mt) cc_final: 0.7956 (tt) REVERT: B 378 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8451 (tppt) REVERT: B 383 GLN cc_start: 0.9163 (tt0) cc_final: 0.8898 (mt0) REVERT: B 415 GLN cc_start: 0.7871 (mt0) cc_final: 0.6738 (mt0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1672 time to fit residues: 28.8653 Evaluate side-chains 111 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.0070 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5072 Z= 0.183 Angle : 0.699 8.511 7024 Z= 0.337 Chirality : 0.043 0.320 964 Planarity : 0.004 0.039 812 Dihedral : 7.272 59.857 1629 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.30 (0.34), residues: 670 helix: 0.94 (0.27), residues: 396 sheet: -0.48 (0.92), residues: 39 loop : -2.16 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 146 HIS 0.004 0.001 HIS B 632 PHE 0.018 0.001 PHE B 436 TYR 0.013 0.001 TYR A 88 ARG 0.002 0.000 ARG B 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1340 Ramachandran restraints generated. 670 Oldfield, 0 Emsley, 670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7642 (m) cc_final: 0.7336 (p) REVERT: A 31 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7777 (ptp-170) REVERT: A 103 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7785 (tpp80) REVERT: A 104 GLU cc_start: 0.8050 (tp30) cc_final: 0.7620 (pt0) REVERT: A 132 GLN cc_start: 0.6421 (mm110) cc_final: 0.5813 (mm110) REVERT: A 133 LEU cc_start: 0.7748 (tp) cc_final: 0.7392 (tp) REVERT: A 166 THR cc_start: 0.9220 (m) cc_final: 0.8847 (m) REVERT: A 170 GLN cc_start: 0.8459 (pm20) cc_final: 0.7670 (pm20) REVERT: A 209 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8635 (tp-100) REVERT: B 16 TYR cc_start: 0.8534 (t80) cc_final: 0.8109 (t80) REVERT: B 300 TYR cc_start: 0.8595 (t80) cc_final: 0.8267 (t80) REVERT: B 304 ARG cc_start: 0.8139 (tpt90) cc_final: 0.7793 (tpp80) REVERT: B 329 MET cc_start: 0.8006 (mtm) cc_final: 0.7666 (mmp) REVERT: B 347 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7078 (tp30) REVERT: B 359 GLU cc_start: 0.7945 (mp0) cc_final: 0.7615 (mp0) REVERT: B 362 LEU cc_start: 0.8455 (mt) cc_final: 0.7829 (tt) REVERT: B 378 LYS cc_start: 0.9108 (mtpp) cc_final: 0.8667 (tppt) REVERT: B 383 GLN cc_start: 0.9151 (tt0) cc_final: 0.8901 (mt0) REVERT: B 415 GLN cc_start: 0.7779 (mt0) cc_final: 0.6873 (mt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1804 time to fit residues: 32.6433 Evaluate side-chains 115 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS B 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.147873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.120098 restraints weight = 12549.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123175 restraints weight = 7369.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125232 restraints weight = 5278.844| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5072 Z= 0.208 Angle : 0.693 7.813 7024 Z= 0.338 Chirality : 0.043 0.327 964 Planarity : 0.004 0.035 812 Dihedral : 7.220 59.656 1629 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.67 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.22 (0.34), residues: 670 helix: 0.99 (0.26), residues: 396 sheet: -0.44 (0.92), residues: 39 loop : -2.11 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 146 HIS 0.004 0.002 HIS A 99 PHE 0.020 0.001 PHE B 436 TYR 0.015 0.001 TYR A 88 ARG 0.005 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.34 seconds wall clock time: 25 minutes 5.06 seconds (1505.06 seconds total)