Starting phenix.real_space_refine on Wed Feb 12 13:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5u_38953/02_2025/8y5u_38953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5u_38953/02_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_38953/02_2025/8y5u_38953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5u_38953/02_2025/8y5u_38953.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5u_38953/02_2025/8y5u_38953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5u_38953/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.95, per 1000 atoms: 0.62 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: 2.24 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: 0.74 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: 2.32 Time building geometry restraints manager: 2.52 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.320 Find NCS groups from input model: 0.330 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 : 0.917 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: 0.1594 time to fit residues: 30.9956 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 : 0.833 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110650 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: 0.8403 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 : 0.849 Fit side-chains REVERT: A 127 PHE cc_start: 0.7260 (m-80) cc_final: 0.6670 (m-10) REVERT: A 237 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7251 (ptp-110) REVERT: A 362 PHE cc_start: 0.7126 (p90) cc_final: 0.6722 (t80) outliers start: 9 outliers final: 7 residues processed: 125 average time/residue: 0.1670 time to fit residues: 30.3729 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 : 0.842 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 88 optimal weight: 0.0170 chunk 93 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.144061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110644 restraints weight = 11146.097| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.28 r_work: 0.3218 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1189 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= 0.176 Angle : 0.542 8.301 11182 Z= 0.277 Chirality : 0.039 0.150 1342 Planarity : 0.006 0.063 1330 Dihedral : 4.115 31.851 1053 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 0.92 % Allowed : 10.82 % Favored : 88.26 % 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: 1.92 (0.28), residues: 998 helix: 2.15 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 372 HIS 0.004 0.001 HIS A 31 PHE 0.027 0.001 PHE A 362 TYR 0.007 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 133 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.933 Fit side-chains REVERT: A 127 PHE cc_start: 0.7227 (m-80) cc_final: 0.6612 (m-10) REVERT: A 250 ILE cc_start: 0.8184 (mm) cc_final: 0.7961 (mt) REVERT: A 362 PHE cc_start: 0.7039 (p90) cc_final: 0.6812 (t80) REVERT: A 514 TYR cc_start: 0.8368 (t80) cc_final: 0.8156 (t80) REVERT: B 417 ASP cc_start: 0.8038 (p0) cc_final: 0.7828 (p0) outliers start: 8 outliers final: 6 residues processed: 129 average time/residue: 0.1654 time to fit residues: 30.5853 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 508 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.142797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108238 restraints weight = 11102.999| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.34 r_work: 0.3173 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1294 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= 0.225 Angle : 0.569 9.348 11182 Z= 0.290 Chirality : 0.040 0.158 1342 Planarity : 0.005 0.064 1330 Dihedral : 4.173 30.621 1053 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 1.73 % Allowed : 12.66 % Favored : 85.62 % 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: 1.89 (0.28), residues: 998 helix: 2.13 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 PHE 0.025 0.001 PHE A 362 TYR 0.014 0.001 TYR B 542 ARG 0.002 0.000 ARG A 237 *********************** 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 134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.848 Fit side-chains REVERT: A 127 PHE cc_start: 0.7174 (m-80) cc_final: 0.6584 (m-10) REVERT: A 237 ARG cc_start: 0.7639 (mtp180) cc_final: 0.7306 (ptp-110) REVERT: A 250 ILE cc_start: 0.8143 (mm) cc_final: 0.7887 (mt) REVERT: B 417 ASP cc_start: 0.7909 (p0) cc_final: 0.7682 (p0) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.1715 time to fit residues: 31.4910 Evaluate side-chains 124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 0.0060 chunk 84 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 536 ASN 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 = 0.143506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109257 restraints weight = 10931.760| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.31 r_work: 0.3182 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1436 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= 0.194 Angle : 0.552 8.841 11182 Z= 0.282 Chirality : 0.039 0.165 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.135 31.813 1053 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 1.50 % Allowed : 12.89 % Favored : 85.62 % 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: 1.92 (0.28), residues: 998 helix: 2.16 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -1.50 (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 0.022 0.001 PHE A 287 TYR 0.008 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 135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.866 Fit side-chains REVERT: A 115 MET cc_start: 0.8484 (tpp) cc_final: 0.7913 (ttm) REVERT: A 127 PHE cc_start: 0.7278 (m-80) cc_final: 0.6618 (m-10) REVERT: A 250 ILE cc_start: 0.8191 (mm) cc_final: 0.7938 (mt) REVERT: A 335 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8488 (mt0) REVERT: B 417 ASP cc_start: 0.7998 (p0) cc_final: 0.7759 (p0) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.1699 time to fit residues: 31.5149 Evaluate side-chains 126 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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: 0.0050 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.143527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109998 restraints weight = 10974.036| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.27 r_work: 0.3204 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1519 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= 0.178 Angle : 0.544 8.396 11182 Z= 0.278 Chirality : 0.039 0.170 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.076 30.769 1053 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 13.35 % Favored : 84.58 % 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: 1.98 (0.28), residues: 998 helix: 2.20 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 572 HIS 0.004 0.001 HIS B 234 PHE 0.020 0.001 PHE A 287 TYR 0.029 0.001 TYR B 514 ARG 0.002 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 146 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.814 Fit side-chains REVERT: A 115 MET cc_start: 0.8518 (tpp) cc_final: 0.7937 (ttm) REVERT: A 127 PHE cc_start: 0.7357 (m-80) cc_final: 0.6689 (m-10) REVERT: A 250 ILE cc_start: 0.8201 (mm) cc_final: 0.7937 (mt) REVERT: A 335 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8505 (mt0) REVERT: A 450 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: A 567 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6086 (mm) REVERT: B 417 ASP cc_start: 0.7982 (p0) cc_final: 0.7766 (p0) REVERT: B 576 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7169 (pmm) outliers start: 18 outliers final: 13 residues processed: 138 average time/residue: 0.1722 time to fit residues: 34.2952 Evaluate side-chains 132 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.143499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110027 restraints weight = 11068.327| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.30 r_work: 0.3200 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1589 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= 0.191 Angle : 0.556 8.666 11182 Z= 0.284 Chirality : 0.039 0.166 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.075 31.152 1053 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 15.19 % Favored : 82.97 % 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: 2.01 (0.28), residues: 998 helix: 2.22 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 PHE 0.019 0.001 PHE A 287 TYR 0.024 0.001 TYR B 514 ARG 0.001 0.000 ARG B 107 *********************** 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 134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8502 (tpp) cc_final: 0.7888 (ttm) REVERT: A 250 ILE cc_start: 0.8193 (mm) cc_final: 0.7936 (mt) REVERT: A 335 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: A 450 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: A 567 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6030 (mm) REVERT: A 576 MET cc_start: 0.7959 (ptm) cc_final: 0.7654 (ptm) REVERT: B 417 ASP cc_start: 0.8024 (p0) cc_final: 0.7810 (p0) REVERT: B 576 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7242 (pmm) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.1717 time to fit residues: 30.6415 Evaluate side-chains 128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110404 restraints weight = 11188.602| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.32 r_work: 0.3206 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1651 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= 0.183 Angle : 0.555 8.432 11182 Z= 0.283 Chirality : 0.039 0.165 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.049 30.750 1053 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 2.07 % Allowed : 15.07 % Favored : 82.85 % 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: 742 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 372 HIS 0.004 0.001 HIS B 234 PHE 0.017 0.001 PHE A 287 TYR 0.024 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 136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8499 (tpp) cc_final: 0.7892 (ttm) REVERT: A 250 ILE cc_start: 0.8196 (mm) cc_final: 0.7944 (mt) REVERT: A 335 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8511 (mt0) REVERT: A 450 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: A 567 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6023 (mm) REVERT: B 417 ASP cc_start: 0.8000 (p0) cc_final: 0.7795 (p0) REVERT: B 576 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7104 (pmm) REVERT: B 578 ASP cc_start: 0.7921 (t0) cc_final: 0.7646 (t0) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 0.1802 time to fit residues: 32.4856 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 : 0.894 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 30 optimal weight: 0.0050 chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4772 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.144335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111090 restraints weight = 11214.563| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.32 r_work: 0.3216 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1717 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= 0.179 Angle : 0.558 8.284 11182 Z= 0.285 Chirality : 0.040 0.178 1342 Planarity : 0.005 0.062 1330 Dihedral : 4.036 31.041 1053 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 2.07 % Allowed : 15.30 % 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: 2.01 (0.28), residues: 998 helix: 2.22 (0.20), residues: 741 sheet: None (None), residues: 0 loop : -1.41 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 471 HIS 0.004 0.001 HIS B 234 PHE 0.016 0.001 PHE B 354 TYR 0.023 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 142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8413 (tpp) cc_final: 0.7780 (ttm) REVERT: A 250 ILE cc_start: 0.8153 (mm) cc_final: 0.7902 (mt) REVERT: A 335 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: A 450 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: A 567 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6005 (mm) REVERT: B 417 ASP cc_start: 0.7986 (p0) cc_final: 0.7768 (p0) REVERT: B 576 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7065 (pmm) REVERT: B 578 ASP cc_start: 0.7881 (t0) cc_final: 0.7602 (t0) outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 0.1817 time to fit residues: 34.2571 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 : 0.938 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.0040 chunk 85 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 533 ASN ** 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 = 0.3732 r_free = 0.3732 target = 0.143507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110269 restraints weight = 11064.595| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.30 r_work: 0.3203 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1739 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= 0.194 Angle : 0.572 8.529 11182 Z= 0.291 Chirality : 0.040 0.156 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.063 30.862 1053 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 2.07 % Allowed : 15.42 % 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: 2.00 (0.28), residues: 998 helix: 2.20 (0.20), residues: 740 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 471 HIS 0.004 0.001 HIS B 234 PHE 0.015 0.001 PHE A 287 TYR 0.023 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 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8485 (tpp) cc_final: 0.7892 (ttm) REVERT: A 237 ARG cc_start: 0.7609 (mtp180) cc_final: 0.7166 (ptp-110) REVERT: A 250 ILE cc_start: 0.8198 (mm) cc_final: 0.7952 (mt) REVERT: A 331 GLU cc_start: 0.7824 (tp30) cc_final: 0.7363 (tp30) REVERT: A 335 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: A 450 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 567 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6005 (mm) REVERT: B 417 ASP cc_start: 0.8040 (p0) cc_final: 0.7817 (p0) REVERT: B 576 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7056 (pmm) REVERT: B 578 ASP cc_start: 0.8098 (t0) cc_final: 0.7815 (t0) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 0.1890 time to fit residues: 33.7768 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 : 0.877 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.143993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110057 restraints weight = 11207.472| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.37 r_work: 0.3180 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1782 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= 0.199 Angle : 0.576 8.743 11182 Z= 0.293 Chirality : 0.040 0.166 1342 Planarity : 0.005 0.063 1330 Dihedral : 4.103 31.164 1053 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % Rotamer: Outliers : 1.96 % Allowed : 15.88 % Favored : 82.16 % 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: 2.24 (0.20), residues: 732 sheet: None (None), residues: 0 loop : -1.32 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 471 HIS 0.004 0.001 HIS B 234 PHE 0.015 0.001 PHE A 287 TYR 0.023 0.001 TYR B 514 ARG 0.002 0.000 ARG A 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4174.72 seconds wall clock time: 74 minutes 35.88 seconds (4475.88 seconds total)