Starting phenix.real_space_refine on Wed Mar 12 13:53:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5u_38953/03_2025/8y5u_38953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5u_38953/03_2025/8y5u_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_38953/03_2025/8y5u_38953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5u_38953/03_2025/8y5u_38953.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5u_38953/03_2025/8y5u_38953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5u_38953/03_2025/8y5u_38953.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' NA': 2, 'SO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.24, per 1000 atoms: 0.66 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: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.79 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: 2.17 Time building geometry restraints manager: 2.41 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 588 or resid 601)) selection = (chain 'B' and (resid 2 through 366 or resid 373 through 404 or resid 415 throug \ h 588 or resid 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: 1.910 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.710 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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= 0.259 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (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 TRP 0.026 0.002 TRP B 372 HIS 0.003 0.001 HIS B 234 PHE 0.012 0.001 PHE B 430 TYR 0.007 0.001 TYR A 418 ARG 0.001 0.000 ARG A 277 *********************** 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 : 0.769 Fit side-chains 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: 0.1551 time to fit residues: 30.3285 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 : 0.891 ------------------------------------------------------------------------------- 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 85 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3766 r_free = 0.3766 target = 0.144592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110649 restraints weight = 11118.435| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.24 r_work: 0.3215 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0873 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= 0.202 Angle : 0.572 8.750 11182 Z= 0.295 Chirality : 0.040 0.153 1342 Planarity : 0.006 0.063 1330 Dihedral : 4.220 30.272 1055 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.04 % Allowed : 8.63 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.28), residues: 998 helix: 2.19 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 372 HIS 0.005 0.001 HIS A 31 PHE 0.029 0.001 PHE A 362 TYR 0.013 0.001 TYR B 542 ARG 0.003 0.001 ARG B 107 *********************** 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 130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.839 Fit side-chains REVERT: A 127 PHE cc_start: 0.7260 (m-80) cc_final: 0.6669 (m-10) REVERT: A 237 ARG cc_start: 0.7642 (mtp180) cc_final: 0.7250 (ptp-110) REVERT: A 362 PHE cc_start: 0.7126 (p90) cc_final: 0.6721 (t80) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1582 time to fit residues: 28.7538 Evaluate side-chains 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 484 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 13 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.109267 restraints weight = 11164.906| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.28 r_work: 0.3197 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1134 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= 0.196 Angle : 0.553 8.813 11182 Z= 0.283 Chirality : 0.039 0.151 1342 Planarity : 0.006 0.063 1330 Dihedral : 4.162 31.730 1053 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.28), residues: 998 helix: 2.19 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -1.46 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 372 HIS 0.004 0.001 HIS A 31 PHE 0.027 0.001 PHE A 362 TYR 0.008 0.001 TYR B 514 ARG 0.003 0.000 ARG B 107 *********************** 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 129 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.806 Fit side-chains REVERT: A 127 PHE cc_start: 0.7254 (m-80) cc_final: 0.6651 (m-10) REVERT: A 250 ILE cc_start: 0.8201 (mm) cc_final: 0.7969 (mt) REVERT: A 362 PHE cc_start: 0.7078 (p90) cc_final: 0.6813 (t80) outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.1596 time to fit residues: 28.8620 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 416 PHE 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 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109402 restraints weight = 11053.873| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.26 r_work: 0.3183 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1245 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= 0.195 Angle : 0.551 8.822 11182 Z= 0.282 Chirality : 0.039 0.166 1342 Planarity : 0.005 0.064 1330 Dihedral : 4.136 31.131 1053 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 1.61 % Allowed : 12.31 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.28), residues: 998 helix: 2.15 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -1.52 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.004 0.001 HIS B 234 PHE 0.026 0.001 PHE A 362 TYR 0.014 0.001 TYR B 542 ARG 0.002 0.000 ARG B 107 *********************** 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 135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.785 Fit side-chains REVERT: A 127 PHE cc_start: 0.7307 (m-80) cc_final: 0.6632 (m-10) REVERT: A 250 ILE cc_start: 0.8210 (mm) cc_final: 0.7927 (mt) REVERT: A 253 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 362 PHE cc_start: 0.7091 (p90) cc_final: 0.6842 (t80) REVERT: B 417 ASP cc_start: 0.8098 (p0) cc_final: 0.7859 (p0) REVERT: B 578 ASP cc_start: 0.7913 (t0) cc_final: 0.7696 (t0) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.1677 time to fit residues: 31.5047 Evaluate side-chains 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 0.0470 chunk 84 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110529 restraints weight = 11007.245| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.33 r_work: 0.3202 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8185 Z= 0.174 Angle : 0.538 8.308 11182 Z= 0.275 Chirality : 0.039 0.163 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.083 31.258 1053 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 1.50 % Allowed : 12.77 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 998 helix: 2.20 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 424 HIS 0.004 0.001 HIS B 234 PHE 0.026 0.001 PHE A 362 TYR 0.007 0.001 TYR B 39 ARG 0.002 0.000 ARG B 107 *********************** 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 143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.898 Fit side-chains REVERT: A 127 PHE cc_start: 0.7174 (m-80) cc_final: 0.6551 (m-10) REVERT: A 250 ILE cc_start: 0.8128 (mm) cc_final: 0.7844 (mt) REVERT: A 253 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (mt) REVERT: A 335 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: B 417 ASP cc_start: 0.8003 (p0) cc_final: 0.7789 (p0) REVERT: B 578 ASP cc_start: 0.7781 (t0) cc_final: 0.7563 (t0) outliers start: 13 outliers final: 11 residues processed: 138 average time/residue: 0.1645 time to fit residues: 32.8144 Evaluate side-chains 132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3736 r_free = 0.3736 target = 0.143510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110084 restraints weight = 10965.569| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1494 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= 0.186 Angle : 0.544 8.405 11182 Z= 0.279 Chirality : 0.039 0.167 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.062 30.550 1053 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 13.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 998 helix: 2.23 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 PHE 0.025 0.001 PHE A 362 TYR 0.030 0.001 TYR B 514 ARG 0.001 0.000 ARG B 107 *********************** 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 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.812 Fit side-chains REVERT: A 115 MET cc_start: 0.8507 (tpp) cc_final: 0.7917 (ttm) REVERT: A 127 PHE cc_start: 0.7331 (m-80) cc_final: 0.6680 (m-10) REVERT: A 250 ILE cc_start: 0.8193 (mm) cc_final: 0.7894 (mt) REVERT: A 253 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 335 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: A 450 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: A 567 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6955 (tp) REVERT: B 417 ASP cc_start: 0.8038 (p0) cc_final: 0.7793 (p0) REVERT: B 578 ASP cc_start: 0.7965 (t0) cc_final: 0.7738 (t0) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.1595 time to fit residues: 30.5896 Evaluate side-chains 128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3721 r_free = 0.3721 target = 0.142320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.108813 restraints weight = 11090.341| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.31 r_work: 0.3181 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8185 Z= 0.218 Angle : 0.569 9.114 11182 Z= 0.291 Chirality : 0.040 0.169 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.117 31.167 1053 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 1.96 % Allowed : 15.42 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.28), residues: 998 helix: 2.20 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 372 HIS 0.005 0.001 HIS B 234 PHE 0.019 0.001 PHE A 287 TYR 0.027 0.001 TYR B 514 ARG 0.001 0.000 ARG B 237 *********************** 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 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8506 (tpp) cc_final: 0.7907 (ttm) REVERT: A 250 ILE cc_start: 0.8212 (mm) cc_final: 0.7923 (mt) REVERT: A 253 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 335 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: A 450 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: A 514 TYR cc_start: 0.8305 (t80) cc_final: 0.8103 (t80) REVERT: A 567 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6066 (mm) REVERT: A 576 MET cc_start: 0.7986 (ptm) cc_final: 0.7682 (ptm) REVERT: B 417 ASP cc_start: 0.8071 (p0) cc_final: 0.7848 (p0) REVERT: B 576 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7318 (pmm) REVERT: B 578 ASP cc_start: 0.8014 (t0) cc_final: 0.7744 (t0) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 0.1702 time to fit residues: 31.6934 Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 256 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 42 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 0.0470 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 536 ASN ** 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 = 0.3742 r_free = 0.3742 target = 0.144071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110742 restraints weight = 11187.522| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.33 r_work: 0.3213 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8185 Z= 0.177 Angle : 0.549 8.230 11182 Z= 0.283 Chirality : 0.039 0.172 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.066 30.947 1053 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.73 % Allowed : 15.77 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 998 helix: 2.22 (0.20), residues: 741 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 300 HIS 0.004 0.001 HIS B 234 PHE 0.017 0.001 PHE A 287 TYR 0.026 0.001 TYR B 514 ARG 0.001 0.000 ARG B 107 *********************** 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 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8427 (tpp) cc_final: 0.7790 (ttm) REVERT: A 250 ILE cc_start: 0.8136 (mm) cc_final: 0.7828 (mt) REVERT: A 253 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7917 (mp) REVERT: A 335 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: A 450 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 567 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6022 (mm) REVERT: B 576 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7197 (pmm) REVERT: B 578 ASP cc_start: 0.7861 (t0) cc_final: 0.7598 (t0) outliers start: 15 outliers final: 10 residues processed: 130 average time/residue: 0.1822 time to fit residues: 33.9038 Evaluate side-chains 131 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 472 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 12 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109931 restraints weight = 11214.486| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.32 r_work: 0.3199 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1671 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= 0.198 Angle : 0.565 8.622 11182 Z= 0.290 Chirality : 0.040 0.157 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.091 31.127 1053 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 16.11 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 998 helix: 2.21 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 300 HIS 0.004 0.001 HIS B 234 PHE 0.037 0.001 PHE A 362 TYR 0.025 0.001 TYR B 514 ARG 0.001 0.000 ARG B 107 *********************** 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 135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8438 (tpp) cc_final: 0.7806 (ttm) REVERT: A 250 ILE cc_start: 0.8168 (mm) cc_final: 0.7867 (mt) REVERT: A 253 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 335 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8459 (mt0) REVERT: A 450 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 567 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6019 (mm) REVERT: B 576 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7190 (pmm) REVERT: B 578 ASP cc_start: 0.7913 (t0) cc_final: 0.7657 (t0) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.1773 time to fit residues: 31.8767 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 : 0.870 ------------------------------------------------------------------------------- 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 567 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 256 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 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 100 optimal weight: 0.0770 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111890 restraints weight = 11060.451| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.31 r_work: 0.3230 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8185 Z= 0.177 Angle : 0.555 7.928 11182 Z= 0.286 Chirality : 0.040 0.178 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.055 30.994 1053 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 16.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 998 helix: 2.25 (0.20), residues: 739 sheet: None (None), residues: 0 loop : -1.21 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 PHE 0.015 0.001 PHE B 354 TYR 0.025 0.001 TYR B 514 ARG 0.001 0.000 ARG B 107 ********************** 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 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8409 (tpp) cc_final: 0.7783 (ttm) REVERT: A 250 ILE cc_start: 0.8125 (mm) cc_final: 0.7863 (mt) REVERT: A 331 GLU cc_start: 0.7781 (tp30) cc_final: 0.7298 (tp30) REVERT: A 335 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7922 (mp10) REVERT: A 337 TYR cc_start: 0.8333 (t80) cc_final: 0.8050 (t80) REVERT: A 450 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: A 567 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.5992 (mm) REVERT: B 417 ASP cc_start: 0.7768 (p0) cc_final: 0.7516 (p0) REVERT: B 576 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7162 (pmm) REVERT: B 578 ASP cc_start: 0.8005 (t0) cc_final: 0.7774 (t0) outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 0.1743 time to fit residues: 32.3442 Evaluate side-chains 134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 567 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 256 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 61 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.0170 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 40 optimal weight: 0.0370 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115277 restraints weight = 11193.643| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.00 r_work: 0.3263 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1876 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= 0.171 Angle : 0.553 7.870 11182 Z= 0.282 Chirality : 0.040 0.180 1342 Planarity : 0.005 0.063 1330 Dihedral : 3.998 30.580 1053 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 16.34 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.29), residues: 998 helix: 2.31 (0.20), residues: 739 sheet: None (None), residues: 0 loop : -1.25 (0.43), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 PHE 0.026 0.001 PHE A 362 TYR 0.025 0.001 TYR B 514 ARG 0.001 0.000 ARG A 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4449.17 seconds wall clock time: 76 minutes 57.82 seconds (4617.82 seconds total)