Starting phenix.real_space_refine on Thu Jul 2 01:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.cif Found real_map, /net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.cif" model { file = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7etw_31303/07_2026/7etw_31303.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASP:plan': 10, 'ARG:plan': 18, 'GLN:plan1': 11, 'GLU:plan': 13, 'TRP:plan': 6, 'TYR:plan': 8, 'PHE:plan': 10, 'HIS:plan': 11, 'ASN:plan1': 5} 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 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: 1.34, per 1000 atoms: 0.27 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: 0.49 Conformation dependent library (CDL) restraints added in 212.1 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: 0.08 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: 0.66 Time building geometry restraints manager: 0.57 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 - 16.49: 2505 16.49 - 32.98: 174 32.98 - 49.47: 35 49.47 - 65.96: 8 65.96 - 82.45: 4 Dihedral angle restraints: 2726 sinusoidal: 761 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 2723 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 0.130 5074 Z= 0.562 Angle : 1.271 26.896 7030 Z= 0.694 Chirality : 0.076 1.272 964 Planarity : 0.008 0.135 812 Dihedral : 13.248 82.452 1452 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG B 631 TYR 0.027 0.002 TYR A 88 PHE 0.013 0.002 PHE A 155 TRP 0.016 0.002 TRP B 633 HIS 0.024 0.004 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.55 ( 5072) covalent geometry : angle 1.20659 / 0.68 ( 7024) hydrogen bonds : bond 0.19711 / 12.65 ( 289) hydrogen bonds : angle 7.91686 / 5.72 ( 852) link_BETA1-4 : bond 0.05138 / 2.70 ( 1) link_BETA1-4 : angle 10.47834 / 4.72 ( 3) link_NAG-ASN : bond 0.12959 / 6.82 ( 1) link_NAG-ASN : angle 16.28184 / 7.94 ( 3) *********************** 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 : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7211 (ptp-170) REVERT: A 93 ARG cc_start: 0.7952 (ttt90) cc_final: 0.6894 (tmt170) REVERT: A 167 VAL cc_start: 0.9082 (t) cc_final: 0.8823 (p) REVERT: A 208 ARG cc_start: 0.8669 (mtt180) cc_final: 0.8095 (mtt180) REVERT: A 209 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7534 (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: 0.7912 (tp30) REVERT: B 442 ILE cc_start: 0.8824 (tp) cc_final: 0.8533 (mm) REVERT: B 445 ARG cc_start: 0.8511 (ttt90) cc_final: 0.8016 (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: 0.7562 (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: 0.0760 time to fit residues: 15.0444 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 : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130496 restraints weight = 13009.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.133868 restraints weight = 7001.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.135950 restraints weight = 4763.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137160 restraints weight = 3702.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138179 restraints weight = 3178.098| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5074 Z= 0.170 Angle : 0.838 7.950 7030 Z= 0.395 Chirality : 0.045 0.318 964 Planarity : 0.005 0.081 812 Dihedral : 4.968 21.230 727 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.42 % Favored : 92.84 % Rotamer: Outliers : 0.27 % Allowed : 7.63 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.30), residues: 670 helix: -0.89 (0.25), residues: 388 sheet: -1.09 (0.86), residues: 37 loop : -3.25 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 103 TYR 0.028 0.003 TYR A 178 PHE 0.021 0.002 PHE B 301 TRP 0.017 0.001 TRP A 146 HIS 0.011 0.002 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 5072) covalent geometry : angle 0.82823 / 0.39 ( 7024) hydrogen bonds : bond 0.05561 / 3.70 ( 289) hydrogen bonds : angle 4.86020 / 3.46 ( 852) link_BETA1-4 : bond 0.00118 / 0.06 ( 1) link_BETA1-4 : angle 1.68113 / 0.84 ( 3) link_NAG-ASN : bond 0.00283 / 0.15 ( 1) link_NAG-ASN : angle 5.92912 / 3.12 ( 3) *********************** 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 144 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7532 (tp-100) REVERT: B 298 TYR cc_start: 0.8476 (t80) cc_final: 0.7388 (t80) REVERT: B 378 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8106 (ttmm) REVERT: B 380 ARG cc_start: 0.8339 (ttt90) cc_final: 0.7897 (ttt180) REVERT: B 383 GLN cc_start: 0.9003 (tt0) cc_final: 0.8446 (mt0) REVERT: B 388 GLU cc_start: 0.8343 (tp30) cc_final: 0.8105 (tp30) REVERT: B 415 GLN cc_start: 0.8536 (mt0) cc_final: 0.7109 (mt0) REVERT: B 442 ILE cc_start: 0.8682 (tp) cc_final: 0.8422 (mm) REVERT: B 445 ARG cc_start: 0.8429 (ttt90) cc_final: 0.7927 (mmm160) REVERT: B 447 MET cc_start: 0.7702 (ttt) cc_final: 0.7416 (ppp) REVERT: B 626 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7406 (mmp80) REVERT: B 627 LYS cc_start: 0.7677 (mttt) cc_final: 0.7462 (pttm) REVERT: B 641 ASN cc_start: 0.5373 (t0) cc_final: 0.5110 (t0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.0625 time to fit residues: 11.2569 Evaluate side-chains 106 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 120 HIS B 632 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129704 restraints weight = 12660.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133078 restraints weight = 7083.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.135219 restraints weight = 4883.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136603 restraints weight = 3859.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137236 restraints weight = 3287.419| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5074 Z= 0.144 Angle : 0.742 8.856 7030 Z= 0.347 Chirality : 0.043 0.253 964 Planarity : 0.004 0.038 812 Dihedral : 4.284 16.574 727 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.37 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.33), residues: 670 helix: 0.30 (0.26), residues: 388 sheet: -0.62 (0.89), residues: 37 loop : -2.74 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 31 TYR 0.019 0.002 TYR A 180 PHE 0.025 0.002 PHE B 420 TRP 0.016 0.001 TRP A 146 HIS 0.023 0.004 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 5072) covalent geometry : angle 0.73486 / 0.35 ( 7024) hydrogen bonds : bond 0.04713 / 3.07 ( 289) hydrogen bonds : angle 4.11251 / 2.93 ( 852) link_BETA1-4 : bond 0.00288 / 0.15 ( 1) link_BETA1-4 : angle 1.72167 / 0.89 ( 3) link_NAG-ASN : bond 0.00803 / 0.42 ( 1) link_NAG-ASN : angle 4.87849 / 2.59 ( 3) *********************** 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 129 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.5835 (mm110) cc_final: 0.5487 (mm110) REVERT: A 166 THR cc_start: 0.9073 (m) cc_final: 0.8523 (m) REVERT: A 170 GLN cc_start: 0.8428 (pm20) cc_final: 0.7805 (pm20) REVERT: A 209 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7857 (tp-100) REVERT: B 298 TYR cc_start: 0.8643 (t80) cc_final: 0.8137 (t80) REVERT: B 304 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7799 (tpt90) REVERT: B 378 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8236 (ttmm) REVERT: B 383 GLN cc_start: 0.9000 (tt0) cc_final: 0.8598 (mt0) REVERT: B 388 GLU cc_start: 0.8554 (tp30) cc_final: 0.8005 (tp30) REVERT: B 396 MET cc_start: 0.7491 (ttm) cc_final: 0.7268 (ttm) REVERT: B 442 ILE cc_start: 0.8773 (tp) cc_final: 0.8510 (mm) REVERT: B 445 ARG cc_start: 0.8433 (ttt90) cc_final: 0.7834 (mtp-110) REVERT: B 630 PHE cc_start: 0.7787 (t80) cc_final: 0.7367 (m-80) REVERT: B 641 ASN cc_start: 0.5044 (t0) cc_final: 0.4801 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0549 time to fit residues: 9.0374 Evaluate side-chains 108 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 34 optimal weight: 30.0000 chunk 37 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122664 restraints weight = 12818.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125914 restraints weight = 7182.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127868 restraints weight = 5020.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.128953 restraints weight = 3995.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.129955 restraints weight = 3481.247| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5074 Z= 0.198 Angle : 0.772 7.277 7030 Z= 0.363 Chirality : 0.044 0.278 964 Planarity : 0.004 0.052 812 Dihedral : 4.307 16.899 727 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.87 % Favored : 92.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.33), residues: 670 helix: 0.46 (0.26), residues: 391 sheet: 1.47 (1.15), residues: 22 loop : -2.82 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.042 0.002 TYR A 88 PHE 0.014 0.002 PHE A 197 TRP 0.018 0.001 TRP A 146 HIS 0.006 0.001 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 5072) covalent geometry : angle 0.76676 / 0.36 ( 7024) hydrogen bonds : bond 0.04612 / 3.04 ( 289) hydrogen bonds : angle 4.21670 / 2.99 ( 852) link_BETA1-4 : bond 0.00968 / 0.51 ( 1) link_BETA1-4 : angle 1.09345 / 0.54 ( 3) link_NAG-ASN : bond 0.00932 / 0.49 ( 1) link_NAG-ASN : angle 4.45547 / 2.38 ( 3) *********************** 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 133 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.6631 (mmm) cc_final: 0.6026 (mmm) REVERT: A 132 GLN cc_start: 0.6204 (mm110) cc_final: 0.5868 (mm110) REVERT: A 149 ASP cc_start: 0.8213 (t0) cc_final: 0.7719 (t0) REVERT: A 209 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7931 (tp-100) REVERT: B 16 TYR cc_start: 0.8192 (t80) cc_final: 0.7655 (t80) REVERT: B 376 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 378 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8121 (ttmm) REVERT: B 383 GLN cc_start: 0.9032 (tt0) cc_final: 0.8692 (mt0) REVERT: B 388 GLU cc_start: 0.8679 (tp30) cc_final: 0.8392 (tp30) REVERT: B 396 MET cc_start: 0.7509 (ttm) cc_final: 0.7192 (ttm) REVERT: B 442 ILE cc_start: 0.8843 (tp) cc_final: 0.8611 (mm) REVERT: B 445 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8259 (ttt-90) REVERT: B 447 MET cc_start: 0.7945 (ttt) cc_final: 0.7232 (ppp) REVERT: B 641 ASN cc_start: 0.5383 (t0) cc_final: 0.5103 (t0) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0569 time to fit residues: 9.7168 Evaluate side-chains 103 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 44 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 42 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.150892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.122937 restraints weight = 12792.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126384 restraints weight = 6994.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.128536 restraints weight = 4836.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129682 restraints weight = 3833.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130685 restraints weight = 3321.359| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5074 Z= 0.126 Angle : 0.696 9.347 7030 Z= 0.324 Chirality : 0.041 0.232 964 Planarity : 0.004 0.041 812 Dihedral : 4.049 16.875 727 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.67 % Favored : 93.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.34), residues: 670 helix: 0.85 (0.27), residues: 391 sheet: -0.54 (0.90), residues: 37 loop : -2.52 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 103 TYR 0.016 0.001 TYR A 178 PHE 0.016 0.001 PHE A 41 TRP 0.015 0.001 TRP A 146 HIS 0.008 0.002 HIS B 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 5072) covalent geometry : angle 0.69168 / 0.32 ( 7024) hydrogen bonds : bond 0.04097 / 2.71 ( 289) hydrogen bonds : angle 3.88812 / 2.74 ( 852) link_BETA1-4 : bond 0.00219 / 0.12 ( 1) link_BETA1-4 : angle 1.05465 / 0.54 ( 3) link_NAG-ASN : bond 0.00662 / 0.35 ( 1) link_NAG-ASN : angle 3.68099 / 1.95 ( 3) *********************** 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 137 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.9176 (mp) cc_final: 0.8973 (mt) REVERT: A 132 GLN cc_start: 0.6198 (mm110) cc_final: 0.5693 (mm110) REVERT: A 149 ASP cc_start: 0.8251 (t0) cc_final: 0.7995 (t70) REVERT: A 208 ARG cc_start: 0.8987 (mtp180) cc_final: 0.8693 (mtp180) REVERT: A 209 GLN cc_start: 0.8651 (tp-100) cc_final: 0.8121 (tp-100) REVERT: B 16 TYR cc_start: 0.8239 (t80) cc_final: 0.7634 (t80) REVERT: B 298 TYR cc_start: 0.9058 (t80) cc_final: 0.8641 (t80) REVERT: B 359 GLU cc_start: 0.7697 (mp0) cc_final: 0.7430 (mp0) REVERT: B 362 LEU cc_start: 0.8682 (mt) cc_final: 0.8013 (tt) REVERT: B 383 GLN cc_start: 0.9064 (tt0) cc_final: 0.8732 (mt0) REVERT: B 396 MET cc_start: 0.7483 (ttm) cc_final: 0.7203 (ttm) REVERT: B 442 ILE cc_start: 0.8803 (tp) cc_final: 0.8581 (mm) REVERT: B 445 ARG cc_start: 0.8288 (ttt90) cc_final: 0.8048 (ttt-90) REVERT: B 447 MET cc_start: 0.7957 (ttt) cc_final: 0.7196 (ppp) REVERT: B 449 LEU cc_start: 0.8734 (mt) cc_final: 0.8451 (mt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0570 time to fit residues: 10.1865 Evaluate side-chains 113 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.0050 chunk 8 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 120 HIS B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.150305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122056 restraints weight = 13113.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.125466 restraints weight = 7271.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127651 restraints weight = 5063.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129128 restraints weight = 4008.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129848 restraints weight = 3434.787| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5074 Z= 0.141 Angle : 0.700 6.633 7030 Z= 0.333 Chirality : 0.042 0.235 964 Planarity : 0.004 0.035 812 Dihedral : 4.004 15.838 727 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.67 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.33), residues: 670 helix: 0.89 (0.27), residues: 391 sheet: -0.40 (0.92), residues: 37 loop : -2.44 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.031 0.002 TYR A 88 PHE 0.016 0.002 PHE B 301 TRP 0.015 0.001 TRP A 146 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5072) covalent geometry : angle 0.69577 / 0.33 ( 7024) hydrogen bonds : bond 0.04182 / 2.76 ( 289) hydrogen bonds : angle 3.93460 / 2.81 ( 852) link_BETA1-4 : bond 0.00418 / 0.22 ( 1) link_BETA1-4 : angle 0.68379 / 0.34 ( 3) link_NAG-ASN : bond 0.00668 / 0.35 ( 1) link_NAG-ASN : angle 3.60929 / 1.92 ( 3) *********************** 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 133 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.165 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 46 LEU cc_start: 0.9220 (mp) cc_final: 0.9014 (mt) REVERT: A 132 GLN cc_start: 0.6129 (mm110) cc_final: 0.5637 (mm110) REVERT: A 166 THR cc_start: 0.9153 (m) cc_final: 0.8631 (m) REVERT: A 170 GLN cc_start: 0.8470 (pm20) cc_final: 0.7534 (pm20) REVERT: A 208 ARG cc_start: 0.9096 (mtp180) cc_final: 0.8617 (mtp180) REVERT: A 209 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8168 (tp-100) REVERT: B 16 TYR cc_start: 0.8181 (t80) cc_final: 0.7841 (t80) REVERT: B 298 TYR cc_start: 0.9101 (t80) cc_final: 0.8646 (t80) REVERT: B 359 GLU cc_start: 0.7752 (mp0) cc_final: 0.7502 (mp0) REVERT: B 362 LEU cc_start: 0.8676 (mt) cc_final: 0.8001 (tt) REVERT: B 383 GLN cc_start: 0.9040 (tt0) cc_final: 0.8735 (mt0) REVERT: B 396 MET cc_start: 0.7337 (ttm) cc_final: 0.7136 (ttm) REVERT: B 442 ILE cc_start: 0.8870 (tp) cc_final: 0.8651 (mm) REVERT: B 630 PHE cc_start: 0.7577 (t80) cc_final: 0.7295 (m-80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0526 time to fit residues: 9.0654 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 40 optimal weight: 30.0000 chunk 20 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 66 optimal weight: 50.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 120 HIS B 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121616 restraints weight = 12805.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124963 restraints weight = 7165.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127098 restraints weight = 4999.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.128147 restraints weight = 3985.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129159 restraints weight = 3492.216| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5074 Z= 0.145 Angle : 0.714 7.276 7030 Z= 0.340 Chirality : 0.043 0.232 964 Planarity : 0.004 0.037 812 Dihedral : 4.015 15.838 727 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.97 % Favored : 93.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.34), residues: 670 helix: 0.96 (0.27), residues: 394 sheet: -0.33 (0.93), residues: 37 loop : -2.33 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.025 0.002 TYR B 639 PHE 0.018 0.001 PHE A 41 TRP 0.017 0.001 TRP A 146 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5072) covalent geometry : angle 0.71015 / 0.34 ( 7024) hydrogen bonds : bond 0.04110 / 2.71 ( 289) hydrogen bonds : angle 3.96423 / 2.80 ( 852) link_BETA1-4 : bond 0.00355 / 0.19 ( 1) link_BETA1-4 : angle 0.82579 / 0.42 ( 3) link_NAG-ASN : bond 0.00663 / 0.35 ( 1) link_NAG-ASN : angle 3.50771 / 1.86 ( 3) *********************** 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 136 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7655 (m) cc_final: 0.7358 (p) REVERT: A 120 HIS cc_start: 0.8395 (t-90) cc_final: 0.8143 (t-170) REVERT: A 132 GLN cc_start: 0.6207 (mm110) cc_final: 0.5824 (tt0) REVERT: A 149 ASP cc_start: 0.8415 (t70) cc_final: 0.7829 (t70) REVERT: A 170 GLN cc_start: 0.8411 (pm20) cc_final: 0.7736 (pm20) REVERT: A 209 GLN cc_start: 0.8733 (tp-100) cc_final: 0.8333 (tp-100) REVERT: B 16 TYR cc_start: 0.8233 (t80) cc_final: 0.7872 (t80) REVERT: B 347 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7198 (tp30) REVERT: B 359 GLU cc_start: 0.7649 (mp0) cc_final: 0.7382 (mp0) REVERT: B 362 LEU cc_start: 0.8665 (mt) cc_final: 0.7950 (tt) REVERT: B 378 LYS cc_start: 0.8966 (mttm) cc_final: 0.8399 (tppt) REVERT: B 380 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7873 (ttt-90) REVERT: B 383 GLN cc_start: 0.9049 (tt0) cc_final: 0.8758 (mt0) REVERT: B 396 MET cc_start: 0.7304 (ttm) cc_final: 0.7055 (ttm) REVERT: B 442 ILE cc_start: 0.8877 (tp) cc_final: 0.8644 (mm) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0592 time to fit residues: 10.3936 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 : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 16 optimal weight: 0.0970 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 50.0000 chunk 53 optimal weight: 0.0770 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.152628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127158 restraints weight = 12857.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130694 restraints weight = 6957.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132830 restraints weight = 4727.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134204 restraints weight = 3684.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134817 restraints weight = 3138.185| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5074 Z= 0.126 Angle : 0.689 6.652 7030 Z= 0.329 Chirality : 0.041 0.204 964 Planarity : 0.004 0.036 812 Dihedral : 3.855 14.926 727 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.93 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.34), residues: 670 helix: 1.04 (0.27), residues: 397 sheet: -0.21 (0.93), residues: 37 loop : -2.33 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.021 0.001 TYR A 88 PHE 0.020 0.001 PHE B 420 TRP 0.015 0.001 TRP A 146 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 5072) covalent geometry : angle 0.68616 / 0.33 ( 7024) hydrogen bonds : bond 0.04024 / 2.63 ( 289) hydrogen bonds : angle 3.87843 / 2.73 ( 852) link_BETA1-4 : bond 0.00127 / 0.07 ( 1) link_BETA1-4 : angle 1.10713 / 0.52 ( 3) link_NAG-ASN : bond 0.00485 / 0.26 ( 1) link_NAG-ASN : angle 2.90885 / 1.53 ( 3) *********************** 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 145 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7610 (m) cc_final: 0.7324 (p) REVERT: A 132 GLN cc_start: 0.6204 (mm110) cc_final: 0.5890 (tt0) REVERT: A 208 ARG cc_start: 0.8997 (mtp180) cc_final: 0.8689 (mtp180) REVERT: A 209 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8219 (tp-100) REVERT: B 16 TYR cc_start: 0.8117 (t80) cc_final: 0.7729 (t80) REVERT: B 298 TYR cc_start: 0.9045 (t80) cc_final: 0.8273 (t80) REVERT: B 308 MET cc_start: 0.6916 (mtt) cc_final: 0.6622 (mtm) REVERT: B 347 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7231 (tp30) REVERT: B 359 GLU cc_start: 0.7608 (mp0) cc_final: 0.7340 (mp0) REVERT: B 362 LEU cc_start: 0.8492 (mt) cc_final: 0.7789 (tt) REVERT: B 378 LYS cc_start: 0.9141 (mttm) cc_final: 0.8843 (mtpp) REVERT: B 380 ARG cc_start: 0.8224 (ttt90) cc_final: 0.7869 (ttt-90) REVERT: B 396 MET cc_start: 0.7439 (ttm) cc_final: 0.7191 (ttm) REVERT: B 442 ILE cc_start: 0.8831 (tp) cc_final: 0.8628 (mm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0514 time to fit residues: 9.7252 Evaluate side-chains 116 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.0040 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 34 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.154046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.128296 restraints weight = 12937.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131771 restraints weight = 7204.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.133510 restraints weight = 4933.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135065 restraints weight = 3967.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.135628 restraints weight = 3381.745| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5074 Z= 0.121 Angle : 0.680 7.559 7030 Z= 0.324 Chirality : 0.042 0.210 964 Planarity : 0.004 0.036 812 Dihedral : 3.774 15.261 727 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.93 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.34), residues: 670 helix: 1.13 (0.27), residues: 398 sheet: -0.16 (0.93), residues: 37 loop : -2.33 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.023 0.001 TYR A 88 PHE 0.013 0.001 PHE B 630 TRP 0.016 0.001 TRP A 146 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 5072) covalent geometry : angle 0.67740 / 0.32 ( 7024) hydrogen bonds : bond 0.03930 / 2.57 ( 289) hydrogen bonds : angle 3.79576 / 2.68 ( 852) link_BETA1-4 : bond 0.00286 / 0.15 ( 1) link_BETA1-4 : angle 1.17572 / 0.54 ( 3) link_NAG-ASN : bond 0.00538 / 0.28 ( 1) link_NAG-ASN : angle 2.94378 / 1.56 ( 3) *********************** 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 144 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7629 (m) cc_final: 0.7334 (p) REVERT: A 103 ARG cc_start: 0.7720 (mmt90) cc_final: 0.7414 (mmt-90) REVERT: A 120 HIS cc_start: 0.8620 (t-90) cc_final: 0.8252 (t-170) REVERT: A 209 GLN cc_start: 0.8563 (tp-100) cc_final: 0.8262 (tp-100) REVERT: B 16 TYR cc_start: 0.8030 (t80) cc_final: 0.7678 (t80) REVERT: B 298 TYR cc_start: 0.8974 (t80) cc_final: 0.8138 (t80) REVERT: B 308 MET cc_start: 0.6613 (mtt) cc_final: 0.6346 (mtm) REVERT: B 347 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7293 (tp30) REVERT: B 359 GLU cc_start: 0.7516 (mp0) cc_final: 0.7288 (mp0) REVERT: B 362 LEU cc_start: 0.8504 (mt) cc_final: 0.7687 (tt) REVERT: B 378 LYS cc_start: 0.9081 (mttm) cc_final: 0.8689 (mmtt) REVERT: B 380 ARG cc_start: 0.8221 (ttt90) cc_final: 0.7964 (ttt-90) REVERT: B 415 GLN cc_start: 0.7757 (mt0) cc_final: 0.7121 (mp10) REVERT: B 442 ILE cc_start: 0.8764 (tp) cc_final: 0.8563 (mm) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0531 time to fit residues: 9.7677 Evaluate side-chains 117 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 29 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.151991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125560 restraints weight = 12923.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.128858 restraints weight = 7283.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130666 restraints weight = 5088.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132075 restraints weight = 4078.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.133085 restraints weight = 3493.304| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5074 Z= 0.126 Angle : 0.694 8.585 7030 Z= 0.332 Chirality : 0.042 0.217 964 Planarity : 0.004 0.036 812 Dihedral : 3.755 17.380 727 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.78 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.34), residues: 670 helix: 1.18 (0.27), residues: 398 sheet: -0.23 (0.92), residues: 37 loop : -2.28 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.024 0.001 TYR A 88 PHE 0.014 0.001 PHE A 196 TRP 0.016 0.001 TRP A 146 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5072) covalent geometry : angle 0.69095 / 0.33 ( 7024) hydrogen bonds : bond 0.04018 / 2.64 ( 289) hydrogen bonds : angle 3.79070 / 2.68 ( 852) link_BETA1-4 : bond 0.00348 / 0.18 ( 1) link_BETA1-4 : angle 1.13291 / 0.53 ( 3) link_NAG-ASN : bond 0.00531 / 0.28 ( 1) link_NAG-ASN : angle 3.02313 / 1.59 ( 3) ********************** 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 142 residues out of total 597 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.7637 (m) cc_final: 0.7354 (p) REVERT: A 133 LEU cc_start: 0.7459 (tp) cc_final: 0.7151 (tp) REVERT: A 149 ASP cc_start: 0.8622 (t70) cc_final: 0.8108 (t70) REVERT: A 209 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8297 (tp-100) REVERT: B 16 TYR cc_start: 0.8048 (t80) cc_final: 0.7683 (t80) REVERT: B 298 TYR cc_start: 0.9004 (t80) cc_final: 0.8146 (t80) REVERT: B 308 MET cc_start: 0.6713 (mtt) cc_final: 0.6425 (mtm) REVERT: B 347 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7338 (tp30) REVERT: B 359 GLU cc_start: 0.7561 (mp0) cc_final: 0.7310 (mp0) REVERT: B 362 LEU cc_start: 0.8441 (mt) cc_final: 0.7687 (tt) REVERT: B 378 LYS cc_start: 0.9092 (mttm) cc_final: 0.8797 (mmtt) REVERT: B 380 ARG cc_start: 0.8331 (ttt90) cc_final: 0.8110 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.0572 time to fit residues: 10.4927 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 : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 53 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS A 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.126922 restraints weight = 12883.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130283 restraints weight = 7212.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.132130 restraints weight = 5016.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133686 restraints weight = 4026.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.134473 restraints weight = 3415.032| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5074 Z= 0.126 Angle : 0.700 10.389 7030 Z= 0.337 Chirality : 0.043 0.269 964 Planarity : 0.004 0.038 812 Dihedral : 3.749 17.171 727 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.60 % Allowed : 4.48 % Favored : 94.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.34), residues: 670 helix: 1.24 (0.27), residues: 398 sheet: -0.26 (0.91), residues: 37 loop : -2.23 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.009 0.001 TYR A 88 PHE 0.025 0.001 PHE B 435 TRP 0.015 0.001 TRP A 146 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 5072) covalent geometry : angle 0.69678 / 0.34 ( 7024) hydrogen bonds : bond 0.04071 / 2.67 ( 289) hydrogen bonds : angle 3.75755 / 2.67 ( 852) link_BETA1-4 : bond 0.00269 / 0.14 ( 1) link_BETA1-4 : angle 1.19594 / 0.55 ( 3) link_NAG-ASN : bond 0.00512 / 0.27 ( 1) link_NAG-ASN : angle 2.96675 / 1.56 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 867.64 seconds wall clock time: 15 minutes 34.12 seconds (934.12 seconds total)