Starting phenix.real_space_refine on Thu Jul 2 08:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5u_38953/07_2026/8y5u_38953.cif" } resolution = 3.04 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= 0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 Na 3 4.78 5 C 5343 2.51 5 N 1209 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 7961 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3957 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3991 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 480} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 5 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 1.86, per 1000 atoms: 0.23 Number of scatterers: 7961 At special positions: 0 Unit cell: (89.6018, 94.6262, 115.561, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 Na 3 11.00 O 1352 8.00 N 1209 7.00 C 5343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 394.1 milliseconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 1 sheets defined 80.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.569A pdb=" N LEU A 14 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 31 Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 61 through 70 Proline residue: A 67 - end of helix Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 83 through 102 removed outlier: 3.585A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.594A pdb=" N ARG A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 139 through 167 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.925A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 307 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 323 through 341 removed outlier: 3.675A pdb=" N ALA A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 365 removed outlier: 3.951A pdb=" N ASP A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 395 through 398 removed outlier: 3.725A pdb=" N LEU A 398 " --> pdb=" O LEU A 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 398' Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 432 through 452 Processing helix chain 'A' and resid 453 through 463 Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.694A pdb=" N SER A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 489 through 508 Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.694A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 3.856A pdb=" N SER A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 541 Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.706A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.708A pdb=" N MET A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 10 through 23 removed outlier: 3.727A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.885A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 removed outlier: 3.656A pdb=" N LYS B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 61 through 69 Proline residue: B 67 - end of helix Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 83 through 102 removed outlier: 3.551A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 119 through 135 Processing helix chain 'B' and resid 139 through 162 removed outlier: 3.601A pdb=" N MET B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 231 through 246 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.676A pdb=" N LEU B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 307 removed outlier: 3.663A pdb=" N PHE B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.627A pdb=" N MET B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.570A pdb=" N GLY B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.517A pdb=" N ALA B 374 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 removed outlier: 3.712A pdb=" N VAL B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 removed outlier: 3.516A pdb=" N LEU B 398 " --> pdb=" O LEU B 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 398' Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.687A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 452 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 469 through 485 Processing helix chain 'B' and resid 489 through 508 Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix removed outlier: 3.663A pdb=" N ILE B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 Proline residue: B 518 - end of helix removed outlier: 4.176A pdb=" N SER B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 546 through 571 removed outlier: 3.597A pdb=" N MET B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.550A pdb=" N MET B 576 " --> pdb=" O TRP B 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 400 through 403 removed outlier: 6.781A pdb=" N SER B 419 " --> pdb=" O ALA B 401 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1536 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: 1.13 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1203 1.32 - 1.44: 2251 1.44 - 1.57: 4645 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8185 Sorted by residual: bond pdb=" CA SER B 260 " pdb=" C SER B 260 " ideal model delta sigma weight residual 1.523 1.474 0.050 1.30e-02 5.92e+03 1.46e+01 bond pdb=" N THR B 257 " pdb=" CA THR B 257 " ideal model delta sigma weight residual 1.456 1.413 0.043 1.32e-02 5.74e+03 1.07e+01 bond pdb=" CA GLY B 258 " pdb=" C GLY B 258 " ideal model delta sigma weight residual 1.516 1.480 0.036 1.12e-02 7.97e+03 1.03e+01 bond pdb=" C ILE B 256 " pdb=" O ILE B 256 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.23e-02 6.61e+03 9.29e+00 bond pdb=" CA ILE B 256 " pdb=" C ILE B 256 " ideal model delta sigma weight residual 1.522 1.483 0.039 1.38e-02 5.25e+03 7.85e+00 ... (remaining 8180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10930 1.79 - 3.58: 195 3.58 - 5.37: 48 5.37 - 7.17: 7 7.17 - 8.96: 2 Bond angle restraints: 11182 Sorted by residual: angle pdb=" N VAL B 118 " pdb=" CA VAL B 118 " pdb=" C VAL B 118 " ideal model delta sigma weight residual 111.81 107.95 3.86 8.60e-01 1.35e+00 2.02e+01 angle pdb=" C LEU A 23 " pdb=" N LEU A 24 " pdb=" CA LEU A 24 " ideal model delta sigma weight residual 120.06 124.12 -4.06 1.19e+00 7.06e-01 1.16e+01 angle pdb=" C TRP A 361 " pdb=" N PHE A 362 " pdb=" CA PHE A 362 " ideal model delta sigma weight residual 122.65 117.25 5.40 1.60e+00 3.91e-01 1.14e+01 angle pdb=" C THR A 286 " pdb=" N PHE A 287 " pdb=" CA PHE A 287 " ideal model delta sigma weight residual 122.54 117.10 5.44 1.65e+00 3.67e-01 1.09e+01 angle pdb=" C PRO B 530 " pdb=" N VAL B 531 " pdb=" CA VAL B 531 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 ... (remaining 11177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4329 17.64 - 35.29: 363 35.29 - 52.93: 41 52.93 - 70.58: 11 70.58 - 88.22: 3 Dihedral angle restraints: 4747 sinusoidal: 1782 harmonic: 2965 Sorted by residual: dihedral pdb=" CA VAL B 510 " pdb=" C VAL B 510 " pdb=" N ASN B 511 " pdb=" CA ASN B 511 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLN A 346 " pdb=" C GLN A 346 " pdb=" N GLU A 347 " pdb=" CA GLU A 347 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN B 262 " pdb=" CB ASN B 262 " pdb=" CG ASN B 262 " pdb=" OD1 ASN B 262 " ideal model delta sinusoidal sigma weight residual -90.00 -159.00 69.00 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 4744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1197 0.065 - 0.130: 138 0.130 - 0.194: 6 0.194 - 0.259: 0 0.259 - 0.324: 1 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CA ASN B 262 " pdb=" N ASN B 262 " pdb=" C ASN B 262 " pdb=" CB ASN B 262 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CB THR B 261 " pdb=" CA THR B 261 " pdb=" OG1 THR B 261 " pdb=" CG2 THR B 261 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ILE B 508 " pdb=" N ILE B 508 " pdb=" C ILE B 508 " pdb=" CB ILE B 508 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 1339 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 25 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 61 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO A 62 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 502 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 503 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 503 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 503 " -0.034 5.00e-02 4.00e+02 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1135 2.75 - 3.29: 8225 3.29 - 3.83: 13886 3.83 - 4.36: 15684 4.36 - 4.90: 27649 Nonbonded interactions: 66579 Sorted by model distance: nonbonded pdb=" O LYS A 334 " pdb=" NE2 GLN A 338 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLN B 325 " model vdw 2.240 3.040 nonbonded pdb=" O ALA B 59 " pdb=" OH TYR B 81 " model vdw 2.265 3.040 nonbonded pdb=" O PRO A 274 " pdb=" NH1 ARG A 277 " model vdw 2.268 3.120 nonbonded pdb=" OH TYR B 582 " pdb=" O PRO B 587 " model vdw 2.274 3.040 ... (remaining 66574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 161 or (resid 162 through 166 and (name N or nam \ e CA or name C or name O or name CB )) or resid 230 through 316 or resid 323 thr \ ough 601)) selection = (chain 'B' and (resid 2 through 366 or resid 373 through 404 or resid 415 throug \ h 901)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.260 Find NCS groups from input model: 0.150 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.004 0.050 8185 Z= 0.201 Angle : 0.621 8.958 11182 Z= 0.333 Chirality : 0.042 0.324 1342 Planarity : 0.006 0.067 1330 Dihedral : 13.062 88.223 2819 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 0.12 % Allowed : 0.23 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.28), residues: 998 helix: 2.16 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 277 TYR 0.007 0.001 TYR A 418 PHE 0.012 0.001 PHE B 430 TRP 0.026 0.002 TRP B 372 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 ( 8185) covalent geometry : angle 0.62124 / 0.33 (11182) hydrogen bonds : bond 0.11505 / 7.83 ( 516) hydrogen bonds : angle 4.74289 / 3.55 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 511 ASN cc_start: 0.8251 (t0) cc_final: 0.8036 (t0) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.0646 time to fit residues: 12.8415 Evaluate side-chains 109 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 ASN A 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109636 restraints weight = 11150.448| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.21 r_work: 0.3212 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8185 Z= 0.142 Angle : 0.581 9.032 11182 Z= 0.299 Chirality : 0.040 0.151 1342 Planarity : 0.006 0.064 1330 Dihedral : 4.246 30.195 1055 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 0.92 % Allowed : 8.86 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.89 (0.28), residues: 998 helix: 2.16 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 107 TYR 0.013 0.001 TYR B 542 PHE 0.029 0.001 PHE A 362 TRP 0.017 0.001 TRP B 372 HIS 0.006 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8185) covalent geometry : angle 0.58085 / 0.30 (11182) hydrogen bonds : bond 0.04085 / 2.69 ( 516) hydrogen bonds : angle 3.93803 / 2.93 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.293 Fit side-chains REVERT: A 7 ILE cc_start: 0.9117 (mm) cc_final: 0.8913 (pt) REVERT: A 127 PHE cc_start: 0.7268 (m-80) cc_final: 0.6666 (m-10) REVERT: A 237 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7245 (ptp-110) REVERT: A 362 PHE cc_start: 0.7124 (p90) cc_final: 0.6717 (t80) outliers start: 8 outliers final: 6 residues processed: 123 average time/residue: 0.0687 time to fit residues: 12.4577 Evaluate side-chains 124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 508 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.141283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108228 restraints weight = 11041.859| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.17 r_work: 0.3190 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8185 Z= 0.146 Angle : 0.573 9.702 11182 Z= 0.292 Chirality : 0.040 0.157 1342 Planarity : 0.006 0.064 1330 Dihedral : 4.274 32.570 1053 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 1.04 % Allowed : 11.05 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.82 (0.28), residues: 998 helix: 2.11 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.007 0.001 TYR B 514 PHE 0.026 0.001 PHE A 362 TRP 0.014 0.001 TRP B 372 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8185) covalent geometry : angle 0.57337 / 0.29 (11182) hydrogen bonds : bond 0.03932 / 2.59 ( 516) hydrogen bonds : angle 3.79065 / 2.83 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.229 Fit side-chains REVERT: A 253 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8016 (mp) REVERT: B 578 ASP cc_start: 0.7886 (t0) cc_final: 0.7669 (t0) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.0685 time to fit residues: 12.7061 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 ASN A 338 GLN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108063 restraints weight = 11259.940| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.28 r_work: 0.3170 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8185 Z= 0.130 Angle : 0.557 9.183 11182 Z= 0.285 Chirality : 0.039 0.149 1342 Planarity : 0.006 0.063 1330 Dihedral : 4.221 31.393 1053 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.61 % Allowed : 12.08 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.85 (0.28), residues: 998 helix: 2.12 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -1.57 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.014 0.001 TYR B 542 PHE 0.023 0.001 PHE A 287 TRP 0.016 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 8185) covalent geometry : angle 0.55714 / 0.29 (11182) hydrogen bonds : bond 0.03697 / 2.42 ( 516) hydrogen bonds : angle 3.69617 / 2.75 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.307 Fit side-chains REVERT: A 115 MET cc_start: 0.8504 (tpp) cc_final: 0.7836 (mtt) REVERT: A 250 ILE cc_start: 0.8226 (mm) cc_final: 0.8004 (mt) REVERT: A 335 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8513 (mt0) REVERT: B 578 ASP cc_start: 0.7942 (t0) cc_final: 0.7699 (t0) outliers start: 14 outliers final: 10 residues processed: 136 average time/residue: 0.0686 time to fit residues: 13.6767 Evaluate side-chains 130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 572 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107973 restraints weight = 11141.859| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.27 r_work: 0.3168 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8185 Z= 0.131 Angle : 0.562 9.195 11182 Z= 0.287 Chirality : 0.039 0.146 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.194 32.010 1053 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 1.50 % Allowed : 13.58 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.85 (0.28), residues: 998 helix: 2.12 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.007 0.001 TYR B 514 PHE 0.022 0.001 PHE A 287 TRP 0.013 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 8185) covalent geometry : angle 0.56165 / 0.29 (11182) hydrogen bonds : bond 0.03675 / 2.41 ( 516) hydrogen bonds : angle 3.64977 / 2.72 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.309 Fit side-chains REVERT: A 115 MET cc_start: 0.8518 (tpp) cc_final: 0.7895 (mtt) REVERT: A 250 ILE cc_start: 0.8241 (mm) cc_final: 0.7985 (mt) REVERT: A 335 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8506 (mt0) REVERT: B 578 ASP cc_start: 0.7974 (t0) cc_final: 0.7730 (t0) outliers start: 13 outliers final: 12 residues processed: 134 average time/residue: 0.0698 time to fit residues: 13.7438 Evaluate side-chains 126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107895 restraints weight = 11064.094| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.29 r_work: 0.3167 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8185 Z= 0.137 Angle : 0.568 9.356 11182 Z= 0.290 Chirality : 0.039 0.144 1342 Planarity : 0.005 0.064 1330 Dihedral : 4.190 31.422 1053 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.07 % Allowed : 14.04 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.85 (0.28), residues: 998 helix: 2.12 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.028 0.001 TYR B 514 PHE 0.036 0.001 PHE A 362 TRP 0.013 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8185) covalent geometry : angle 0.56756 / 0.29 (11182) hydrogen bonds : bond 0.03701 / 2.42 ( 516) hydrogen bonds : angle 3.62369 / 2.70 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.300 Fit side-chains REVERT: A 115 MET cc_start: 0.8528 (tpp) cc_final: 0.7930 (mtt) REVERT: A 250 ILE cc_start: 0.8217 (mm) cc_final: 0.7972 (mt) REVERT: A 335 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: A 450 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 567 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6944 (tp) REVERT: B 545 LEU cc_start: 0.2252 (OUTLIER) cc_final: 0.2030 (mp) REVERT: B 576 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7422 (pmm) REVERT: B 578 ASP cc_start: 0.8011 (t0) cc_final: 0.7742 (t0) outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.0686 time to fit residues: 13.2382 Evaluate side-chains 129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107797 restraints weight = 11103.780| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.34 r_work: 0.3152 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8185 Z= 0.145 Angle : 0.583 9.527 11182 Z= 0.299 Chirality : 0.040 0.144 1342 Planarity : 0.005 0.064 1330 Dihedral : 4.220 32.128 1053 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.07 % Allowed : 14.73 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.85 (0.28), residues: 998 helix: 2.12 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.025 0.001 TYR B 514 PHE 0.019 0.001 PHE A 287 TRP 0.014 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8185) covalent geometry : angle 0.58306 / 0.30 (11182) hydrogen bonds : bond 0.03771 / 2.46 ( 516) hydrogen bonds : angle 3.62026 / 2.70 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8512 (tpp) cc_final: 0.7945 (mtt) REVERT: A 335 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8495 (mt0) REVERT: A 450 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: A 567 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6899 (tp) REVERT: A 576 MET cc_start: 0.7957 (ptm) cc_final: 0.7611 (ptm) REVERT: B 545 LEU cc_start: 0.2092 (OUTLIER) cc_final: 0.1865 (mp) REVERT: B 576 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7556 (pmm) REVERT: B 578 ASP cc_start: 0.8031 (t0) cc_final: 0.7715 (t0) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 0.0662 time to fit residues: 12.1814 Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 2.9990 chunk 38 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.109921 restraints weight = 11096.124| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.35 r_work: 0.3191 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8185 Z= 0.122 Angle : 0.563 8.705 11182 Z= 0.288 Chirality : 0.039 0.137 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.150 31.926 1053 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 2.42 % Allowed : 14.38 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.93 (0.28), residues: 998 helix: 2.17 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.024 0.001 TYR B 514 PHE 0.035 0.001 PHE A 362 TRP 0.016 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 8185) covalent geometry : angle 0.56255 / 0.29 (11182) hydrogen bonds : bond 0.03486 / 2.27 ( 516) hydrogen bonds : angle 3.56179 / 2.65 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8409 (tpp) cc_final: 0.7818 (mtt) REVERT: A 250 ILE cc_start: 0.8132 (mm) cc_final: 0.7909 (mt) REVERT: A 335 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: A 450 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: A 567 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.5993 (mm) REVERT: B 417 ASP cc_start: 0.7727 (p0) cc_final: 0.7475 (p0) REVERT: B 545 LEU cc_start: 0.2158 (OUTLIER) cc_final: 0.1936 (mp) REVERT: B 576 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7262 (pmm) REVERT: B 578 ASP cc_start: 0.7922 (t0) cc_final: 0.7605 (t0) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.0712 time to fit residues: 13.6436 Evaluate side-chains 133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 0.0170 chunk 77 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109398 restraints weight = 11106.212| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.36 r_work: 0.3185 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8185 Z= 0.128 Angle : 0.579 8.924 11182 Z= 0.296 Chirality : 0.040 0.186 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.154 31.889 1053 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.71 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 15.30 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.93 (0.28), residues: 998 helix: 2.16 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -1.43 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.023 0.001 TYR B 514 PHE 0.017 0.001 PHE A 287 TRP 0.015 0.001 TRP A 300 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8185) covalent geometry : angle 0.57874 / 0.30 (11182) hydrogen bonds : bond 0.03560 / 2.32 ( 516) hydrogen bonds : angle 3.56417 / 2.65 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8413 (tpp) cc_final: 0.7828 (mtt) REVERT: A 335 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8468 (mt0) REVERT: A 450 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 567 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.5992 (mm) REVERT: B 417 ASP cc_start: 0.7722 (p0) cc_final: 0.7467 (p0) REVERT: B 576 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7272 (pmm) REVERT: B 578 ASP cc_start: 0.8019 (t0) cc_final: 0.7691 (t0) outliers start: 20 outliers final: 14 residues processed: 130 average time/residue: 0.0798 time to fit residues: 14.9646 Evaluate side-chains 135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 93 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110761 restraints weight = 11168.904| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.37 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8185 Z= 0.119 Angle : 0.564 8.787 11182 Z= 0.288 Chirality : 0.039 0.154 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.099 31.749 1053 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 1.96 % Allowed : 15.77 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.97 (0.28), residues: 998 helix: 2.17 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.023 0.001 TYR B 514 PHE 0.025 0.001 PHE A 362 TRP 0.024 0.001 TRP A 300 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8185) covalent geometry : angle 0.56360 / 0.29 (11182) hydrogen bonds : bond 0.03400 / 2.20 ( 516) hydrogen bonds : angle 3.52662 / 2.63 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8422 (tpp) cc_final: 0.7861 (mtt) REVERT: A 152 GLU cc_start: 0.7672 (tp30) cc_final: 0.7388 (tp30) REVERT: A 250 ILE cc_start: 0.8080 (mm) cc_final: 0.7861 (mt) REVERT: A 450 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: A 567 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.5975 (mm) REVERT: B 576 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7242 (pmm) REVERT: B 578 ASP cc_start: 0.8087 (t0) cc_final: 0.7768 (t0) outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.0792 time to fit residues: 15.3575 Evaluate side-chains 132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 572 TRP Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109879 restraints weight = 11037.161| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.36 r_work: 0.3191 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8185 Z= 0.129 Angle : 0.576 8.839 11182 Z= 0.293 Chirality : 0.040 0.163 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.116 31.279 1053 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.96 % Allowed : 15.77 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.98 (0.28), residues: 998 helix: 2.18 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.023 0.001 TYR B 514 PHE 0.015 0.001 PHE A 287 TRP 0.031 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8185) covalent geometry : angle 0.57628 / 0.29 (11182) hydrogen bonds : bond 0.03526 / 2.29 ( 516) hydrogen bonds : angle 3.55405 / 2.65 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.71 seconds wall clock time: 35 minutes 2.51 seconds (2102.51 seconds total)