Starting phenix.real_space_refine on Tue Jul 29 21:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.map" model { file = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l48_23157/07_2025/7l48_23157.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 144 5.49 5 S 37 5.16 5 C 6739 2.51 5 N 2052 2.21 5 O 2512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11488 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4229 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 17, 'TRANS': 504} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4181 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 17, 'TRANS': 501} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3074 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 16, 'rna3p': 127} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3837 SG CYS A 475 13.590 59.792 45.199 1.00144.72 S ATOM 4048 SG CYS A 500 11.483 59.182 41.090 1.00168.30 S ATOM 364 SG CYS A 50 53.063 98.075 78.234 1.00132.99 S ATOM 502 SG CYS A 69 56.898 98.778 78.930 1.00109.77 S ATOM 527 SG CYS A 72 55.165 95.811 80.252 1.00111.13 S ATOM 8022 SG CYS B 475 60.243 58.550 15.167 1.00129.53 S ATOM 8043 SG CYS B 478 59.669 57.064 10.831 1.00129.65 S ATOM 4570 SG CYS B 50 29.666 39.470 31.268 1.00448.64 S Time building chain proxies: 9.34, per 1000 atoms: 0.81 Number of scatterers: 11488 At special positions: 0 Unit cell: (101.85, 119.7, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 37 16.00 P 144 15.00 O 2512 8.00 N 2052 7.00 C 6739 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 500 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 475 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 72 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 69 " pdb="ZN ZN A 602 " - pdb=" SG CYS A 50 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 475 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 50 " Number of angles added : 3 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 43.8% alpha, 9.3% beta 47 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.665A pdb=" N ASN A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.335A pdb=" N LYS A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 94 through 126 Processing helix chain 'A' and resid 133 through 153 removed outlier: 4.472A pdb=" N TYR A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.629A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.855A pdb=" N ARG A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.597A pdb=" N GLU A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Processing helix chain 'A' and resid 382 through 414 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.857A pdb=" N MET A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 508 through 519 removed outlier: 4.673A pdb=" N ILE A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 52 through 58 removed outlier: 3.720A pdb=" N ALA B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.242A pdb=" N LYS B 73 " --> pdb=" O CYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 Processing helix chain 'B' and resid 94 through 126 Processing helix chain 'B' and resid 133 through 144 removed outlier: 3.831A pdb=" N VAL B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.807A pdb=" N ALA B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.585A pdb=" N LEU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 3.998A pdb=" N GLY B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 382 through 415 removed outlier: 3.954A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.572A pdb=" N ARG B 429 " --> pdb=" O GLU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 486 through 493 Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.743A pdb=" N ILE B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 4.215A pdb=" N PHE A 214 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 251 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU A 253 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.931A pdb=" N ALA A 49 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 64 " --> pdb=" O ALA A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 7.032A pdb=" N GLY A 323 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.649A pdb=" N TYR B 287 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 345 removed outlier: 5.507A pdb=" N THR B 418 " --> pdb=" O PRO B 319 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 321 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN B 420 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B 323 " --> pdb=" O GLN B 420 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU B 462 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 498 through 500 365 hydrogen bonds defined for protein. 1065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2651 1.34 - 1.46: 3594 1.46 - 1.58: 5439 1.58 - 1.71: 286 1.71 - 1.83: 51 Bond restraints: 12021 Sorted by residual: bond pdb=" CA SER B 51 " pdb=" CB SER B 51 " ideal model delta sigma weight residual 1.529 1.455 0.074 1.59e-02 3.96e+03 2.17e+01 bond pdb=" N LYS A 383 " pdb=" CA LYS A 383 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N LYS B 383 " pdb=" CA LYS B 383 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N LEU A 194 " pdb=" CA LEU A 194 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N LEU A 382 " pdb=" CA LEU A 382 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.14e-02 7.69e+03 7.94e+00 ... (remaining 12016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 16212 2.23 - 4.46: 550 4.46 - 6.69: 87 6.69 - 8.92: 19 8.92 - 11.15: 7 Bond angle restraints: 16875 Sorted by residual: angle pdb=" N GLU B 390 " pdb=" CA GLU B 390 " pdb=" CB GLU B 390 " ideal model delta sigma weight residual 110.12 118.78 -8.66 1.47e+00 4.63e-01 3.47e+01 angle pdb=" C PHE A 435 " pdb=" N ASN A 436 " pdb=" CA ASN A 436 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 angle pdb=" N GLN B 88 " pdb=" CA GLN B 88 " pdb=" CB GLN B 88 " ideal model delta sigma weight residual 110.13 118.64 -8.51 1.48e+00 4.57e-01 3.31e+01 angle pdb=" C PRO B 219 " pdb=" N PHE B 220 " pdb=" CA PHE B 220 " ideal model delta sigma weight residual 122.20 130.82 -8.62 1.72e+00 3.38e-01 2.51e+01 angle pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 ... (remaining 16870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 6997 35.72 - 71.44: 426 71.44 - 107.16: 48 107.16 - 142.88: 2 142.88 - 178.60: 3 Dihedral angle restraints: 7476 sinusoidal: 4409 harmonic: 3067 Sorted by residual: dihedral pdb=" O4' U E 92 " pdb=" C1' U E 92 " pdb=" N1 U E 92 " pdb=" C2 U E 92 " ideal model delta sinusoidal sigma weight residual 232.00 53.40 178.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C E 77 " pdb=" C1' C E 77 " pdb=" N1 C E 77 " pdb=" C2 C E 77 " ideal model delta sinusoidal sigma weight residual 232.00 55.26 176.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U E 110 " pdb=" C1' U E 110 " pdb=" N1 U E 110 " pdb=" C2 U E 110 " ideal model delta sinusoidal sigma weight residual -160.00 -56.82 -103.18 1 1.50e+01 4.44e-03 5.24e+01 ... (remaining 7473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1733 0.089 - 0.179: 181 0.179 - 0.268: 26 0.268 - 0.357: 2 0.357 - 0.446: 2 Chirality restraints: 1944 Sorted by residual: chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CA CYS A 50 " pdb=" N CYS A 50 " pdb=" C CYS A 50 " pdb=" CB CYS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C3' A E 129 " pdb=" C4' A E 129 " pdb=" O3' A E 129 " pdb=" C2' A E 129 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1941 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 52 " 0.025 2.00e-02 2.50e+03 5.20e-02 2.71e+01 pdb=" C LYS B 52 " -0.090 2.00e-02 2.50e+03 pdb=" O LYS B 52 " 0.033 2.00e-02 2.50e+03 pdb=" N HIS B 53 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 48 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLU B 48 " 0.065 2.00e-02 2.50e+03 pdb=" O GLU B 48 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 49 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 84 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 84 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 84 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 85 " 0.021 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2561 2.79 - 3.32: 10342 3.32 - 3.85: 21243 3.85 - 4.37: 24108 4.37 - 4.90: 36428 Nonbonded interactions: 94682 Sorted by model distance: nonbonded pdb=" OG SER B 51 " pdb=" CD ARG B 66 " model vdw 2.263 3.440 nonbonded pdb=" O ASN A 133 " pdb=" OG SER A 136 " model vdw 2.273 3.040 nonbonded pdb=" N6 A E 100 " pdb=" O2 C E 123 " model vdw 2.283 3.120 nonbonded pdb=" OG SER A 476 " pdb=" ND2 ASN A 512 " model vdw 2.298 3.120 nonbonded pdb=" C SER B 51 " pdb=" OG SER B 51 " model vdw 2.302 2.616 ... (remaining 94677 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 7 through 260 or (resid 261 through 262 and (name N or nam \ e CA or name C or name O or name CB )) or resid 263 through 294 or (resid 295 th \ rough 297 and (name N or name CA or name C or name O or name CB )) or resid 298 \ or (resid 299 and (name N or name CA or name C or name O or name CB )) or resid \ 300 through 491 or (resid 492 and (name N or name CA or name C or name O or name \ CB )) or resid 493 through 525 or resid 601 through 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 46.830 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 38.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.008 0.692 12030 Z= 0.335 Angle : 0.969 11.153 16878 Z= 0.548 Chirality : 0.058 0.446 1944 Planarity : 0.006 0.061 1620 Dihedral : 20.408 178.601 5486 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.21 % Cbeta Deviations : 0.20 % 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: -3.57 (0.21), residues: 1037 helix: -1.48 (0.20), residues: 441 sheet: -2.30 (0.40), residues: 132 loop : -3.27 (0.22), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 223 HIS 0.028 0.003 HIS B 210 PHE 0.060 0.003 PHE A 354 TYR 0.032 0.002 TYR B 121 ARG 0.010 0.001 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.14342 ( 479) hydrogen bonds : angle 6.55054 ( 1281) metal coordination : bond 0.23892 ( 9) metal coordination : angle 6.88555 ( 3) covalent geometry : bond 0.00451 (12021) covalent geometry : angle 0.96488 (16875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 TYR cc_start: 0.8106 (t80) cc_final: 0.7831 (t80) REVERT: A 421 MET cc_start: 0.7801 (tmm) cc_final: 0.7521 (tmm) REVERT: A 510 ASP cc_start: 0.8498 (m-30) cc_final: 0.8219 (m-30) REVERT: B 353 HIS cc_start: 0.8389 (t-90) cc_final: 0.8095 (t-170) REVERT: B 358 MET cc_start: 0.8598 (tpt) cc_final: 0.8079 (tpp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.2518 time to fit residues: 31.5663 Evaluate side-chains 53 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.0050 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054523 restraints weight = 61928.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.055958 restraints weight = 32115.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.056778 restraints weight = 21683.183| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12030 Z= 0.140 Angle : 0.587 8.087 16878 Z= 0.310 Chirality : 0.038 0.176 1944 Planarity : 0.004 0.043 1620 Dihedral : 21.195 166.862 3334 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.11 % Allowed : 10.80 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1037 helix: -0.01 (0.23), residues: 462 sheet: -2.07 (0.42), residues: 139 loop : -2.90 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 223 HIS 0.007 0.001 HIS B 210 PHE 0.022 0.001 PHE A 341 TYR 0.011 0.001 TYR A 434 ARG 0.003 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 479) hydrogen bonds : angle 4.56438 ( 1281) metal coordination : bond 0.00414 ( 9) metal coordination : angle 1.55218 ( 3) covalent geometry : bond 0.00292 (12021) covalent geometry : angle 0.58682 (16875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8500 (ttt) cc_final: 0.8141 (tpp) REVERT: A 358 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7362 (ptt) REVERT: A 510 ASP cc_start: 0.8444 (m-30) cc_final: 0.8114 (m-30) REVERT: A 515 LEU cc_start: 0.8870 (tp) cc_final: 0.8513 (mt) REVERT: B 326 ASP cc_start: 0.8436 (t0) cc_final: 0.8208 (t0) REVERT: B 353 HIS cc_start: 0.8860 (t-90) cc_final: 0.8378 (t-170) REVERT: B 358 MET cc_start: 0.8906 (tpt) cc_final: 0.8612 (tpp) outliers start: 10 outliers final: 7 residues processed: 80 average time/residue: 0.4175 time to fit residues: 49.3065 Evaluate side-chains 64 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 232 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 349 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.070828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051524 restraints weight = 62054.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052858 restraints weight = 33560.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053635 restraints weight = 23393.496| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12030 Z= 0.181 Angle : 0.596 7.120 16878 Z= 0.312 Chirality : 0.038 0.159 1944 Planarity : 0.004 0.058 1620 Dihedral : 21.224 167.450 3334 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.34 % Allowed : 13.59 % Favored : 84.08 % 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: -1.61 (0.25), residues: 1037 helix: 0.59 (0.23), residues: 462 sheet: -2.03 (0.42), residues: 137 loop : -2.62 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 443 HIS 0.003 0.001 HIS B 139 PHE 0.034 0.002 PHE A 354 TYR 0.014 0.002 TYR A 122 ARG 0.003 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 479) hydrogen bonds : angle 4.33296 ( 1281) metal coordination : bond 0.00904 ( 9) metal coordination : angle 2.35951 ( 3) covalent geometry : bond 0.00372 (12021) covalent geometry : angle 0.59543 (16875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7724 (tp) REVERT: A 178 MET cc_start: 0.8588 (ttt) cc_final: 0.8373 (ttt) REVERT: A 357 LYS cc_start: 0.9118 (pptt) cc_final: 0.8667 (pptt) REVERT: A 361 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7755 (ttm110) REVERT: A 510 ASP cc_start: 0.8612 (m-30) cc_final: 0.8281 (m-30) REVERT: B 279 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: B 353 HIS cc_start: 0.8835 (t-90) cc_final: 0.8320 (t-170) outliers start: 21 outliers final: 10 residues processed: 75 average time/residue: 0.2294 time to fit residues: 25.9082 Evaluate side-chains 56 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 516 ASN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.070248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051036 restraints weight = 62815.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.052397 restraints weight = 33024.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053128 restraints weight = 22581.584| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12030 Z= 0.197 Angle : 0.604 9.685 16878 Z= 0.314 Chirality : 0.038 0.161 1944 Planarity : 0.004 0.046 1620 Dihedral : 21.304 166.954 3334 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.12 % Allowed : 16.82 % Favored : 81.07 % 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: -1.36 (0.26), residues: 1037 helix: 0.88 (0.24), residues: 462 sheet: -1.98 (0.42), residues: 142 loop : -2.56 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 443 HIS 0.003 0.001 HIS B 139 PHE 0.015 0.002 PHE A 341 TYR 0.013 0.002 TYR B 445 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 479) hydrogen bonds : angle 4.28604 ( 1281) metal coordination : bond 0.01225 ( 9) metal coordination : angle 1.99044 ( 3) covalent geometry : bond 0.00408 (12021) covalent geometry : angle 0.60366 (16875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.9315 (mp) cc_final: 0.9100 (mp) REVERT: A 346 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 510 ASP cc_start: 0.8509 (m-30) cc_final: 0.8226 (m-30) REVERT: B 303 MET cc_start: 0.0761 (ppp) cc_final: 0.0436 (ppp) REVERT: B 326 ASP cc_start: 0.8413 (t0) cc_final: 0.8174 (t0) REVERT: B 353 HIS cc_start: 0.9044 (t-90) cc_final: 0.8527 (t-170) outliers start: 19 outliers final: 14 residues processed: 72 average time/residue: 0.2133 time to fit residues: 23.5893 Evaluate side-chains 66 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 210 HIS A 338 ASN A 371 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.068488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.049335 restraints weight = 63370.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050692 restraints weight = 33346.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051459 restraints weight = 22809.804| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12030 Z= 0.241 Angle : 0.650 10.273 16878 Z= 0.335 Chirality : 0.040 0.279 1944 Planarity : 0.004 0.043 1620 Dihedral : 21.441 167.330 3334 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.90 % Allowed : 18.60 % Favored : 78.51 % 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: -1.40 (0.26), residues: 1037 helix: 0.82 (0.24), residues: 463 sheet: -2.00 (0.42), residues: 143 loop : -2.56 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 443 HIS 0.003 0.001 HIS A 53 PHE 0.017 0.002 PHE B 495 TYR 0.015 0.002 TYR A 434 ARG 0.004 0.001 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 479) hydrogen bonds : angle 4.45721 ( 1281) metal coordination : bond 0.01754 ( 9) metal coordination : angle 2.22032 ( 3) covalent geometry : bond 0.00499 (12021) covalent geometry : angle 0.64978 (16875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.9409 (mp) cc_final: 0.9159 (mp) REVERT: A 510 ASP cc_start: 0.8631 (m-30) cc_final: 0.8330 (m-30) REVERT: B 292 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7060 (ppt90) REVERT: B 326 ASP cc_start: 0.8393 (t0) cc_final: 0.8089 (t0) outliers start: 26 outliers final: 15 residues processed: 73 average time/residue: 0.2166 time to fit residues: 23.9203 Evaluate side-chains 60 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 84 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN A 210 HIS A 369 ASN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.070065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050869 restraints weight = 62703.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052179 restraints weight = 32759.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053065 restraints weight = 22627.837| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12030 Z= 0.158 Angle : 0.597 11.499 16878 Z= 0.303 Chirality : 0.038 0.172 1944 Planarity : 0.004 0.039 1620 Dihedral : 21.320 168.431 3334 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.23 % Allowed : 19.82 % Favored : 77.95 % 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: -1.11 (0.26), residues: 1037 helix: 1.15 (0.24), residues: 461 sheet: -1.93 (0.42), residues: 142 loop : -2.47 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.002 0.001 HIS A 139 PHE 0.009 0.001 PHE B 495 TYR 0.012 0.001 TYR A 82 ARG 0.002 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 479) hydrogen bonds : angle 4.21834 ( 1281) metal coordination : bond 0.00913 ( 9) metal coordination : angle 1.56258 ( 3) covalent geometry : bond 0.00334 (12021) covalent geometry : angle 0.59679 (16875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8806 (t80) cc_final: 0.8297 (t80) REVERT: A 194 LEU cc_start: 0.9374 (mp) cc_final: 0.9117 (mp) REVERT: A 303 MET cc_start: 0.8951 (mmm) cc_final: 0.8635 (mmm) REVERT: A 346 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6554 (mp) REVERT: A 510 ASP cc_start: 0.8417 (m-30) cc_final: 0.8108 (m-30) REVERT: B 326 ASP cc_start: 0.8403 (t0) cc_final: 0.8166 (t0) REVERT: B 353 HIS cc_start: 0.8817 (t-90) cc_final: 0.8491 (t-170) outliers start: 20 outliers final: 12 residues processed: 71 average time/residue: 0.2206 time to fit residues: 24.3341 Evaluate side-chains 62 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 17 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.071042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051445 restraints weight = 62427.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052887 restraints weight = 32093.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053669 restraints weight = 21609.987| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12030 Z= 0.119 Angle : 0.579 12.464 16878 Z= 0.289 Chirality : 0.036 0.172 1944 Planarity : 0.004 0.037 1620 Dihedral : 21.139 168.438 3334 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.34 % Allowed : 20.38 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 1037 helix: 1.38 (0.25), residues: 460 sheet: -1.73 (0.44), residues: 135 loop : -2.39 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.003 0.001 HIS A 139 PHE 0.011 0.001 PHE A 190 TYR 0.011 0.001 TYR A 82 ARG 0.002 0.000 ARG B 13 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 479) hydrogen bonds : angle 4.14626 ( 1281) metal coordination : bond 0.00578 ( 9) metal coordination : angle 1.18095 ( 3) covalent geometry : bond 0.00253 (12021) covalent geometry : angle 0.57869 (16875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8882 (t80) cc_final: 0.8396 (t80) REVERT: A 194 LEU cc_start: 0.9391 (mp) cc_final: 0.9137 (mp) REVERT: A 303 MET cc_start: 0.8911 (mmm) cc_final: 0.8596 (mmm) REVERT: A 346 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6579 (mp) REVERT: A 510 ASP cc_start: 0.8399 (m-30) cc_final: 0.8149 (m-30) REVERT: B 78 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7952 (t70) REVERT: B 292 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7234 (ppt90) REVERT: B 326 ASP cc_start: 0.8531 (t0) cc_final: 0.8185 (t0) REVERT: B 353 HIS cc_start: 0.8777 (t-90) cc_final: 0.8415 (t-170) outliers start: 21 outliers final: 13 residues processed: 78 average time/residue: 0.2186 time to fit residues: 25.6418 Evaluate side-chains 69 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 0.9980 chunk 110 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 88 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.070482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051280 restraints weight = 62806.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052664 restraints weight = 32936.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053483 restraints weight = 22466.945| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12030 Z= 0.150 Angle : 0.586 11.306 16878 Z= 0.297 Chirality : 0.037 0.185 1944 Planarity : 0.004 0.040 1620 Dihedral : 21.092 168.570 3334 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.45 % Allowed : 20.82 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 1037 helix: 1.39 (0.25), residues: 461 sheet: -1.76 (0.44), residues: 137 loop : -2.27 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 302 HIS 0.002 0.001 HIS B 139 PHE 0.017 0.001 PHE A 214 TYR 0.011 0.001 TYR A 82 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 479) hydrogen bonds : angle 4.15618 ( 1281) metal coordination : bond 0.00931 ( 9) metal coordination : angle 1.48540 ( 3) covalent geometry : bond 0.00315 (12021) covalent geometry : angle 0.58601 (16875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: A 121 TYR cc_start: 0.8852 (t80) cc_final: 0.8354 (t80) REVERT: A 194 LEU cc_start: 0.9367 (mp) cc_final: 0.9110 (mp) REVERT: A 303 MET cc_start: 0.9046 (mmm) cc_final: 0.8820 (mmm) REVERT: A 346 ILE cc_start: 0.7013 (OUTLIER) cc_final: 0.6615 (mp) REVERT: A 448 MET cc_start: 0.8134 (ttp) cc_final: 0.7731 (ptm) REVERT: A 510 ASP cc_start: 0.8419 (m-30) cc_final: 0.8178 (m-30) REVERT: B 78 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7892 (t70) REVERT: B 292 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7225 (ppt90) REVERT: B 303 MET cc_start: 0.0726 (ppp) cc_final: 0.0452 (tmm) REVERT: B 326 ASP cc_start: 0.8513 (t0) cc_final: 0.8204 (t0) REVERT: B 353 HIS cc_start: 0.8828 (t-90) cc_final: 0.8495 (t-170) outliers start: 22 outliers final: 16 residues processed: 75 average time/residue: 0.2435 time to fit residues: 26.8793 Evaluate side-chains 71 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.069716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050550 restraints weight = 64064.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.051924 restraints weight = 33332.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.052750 restraints weight = 22688.332| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12030 Z= 0.172 Angle : 0.609 12.522 16878 Z= 0.308 Chirality : 0.038 0.188 1944 Planarity : 0.004 0.045 1620 Dihedral : 21.094 168.507 3334 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.90 % Allowed : 20.71 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 1037 helix: 1.32 (0.24), residues: 471 sheet: -1.77 (0.44), residues: 137 loop : -2.23 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 443 HIS 0.003 0.001 HIS B 139 PHE 0.024 0.002 PHE A 214 TYR 0.011 0.001 TYR A 434 ARG 0.004 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 479) hydrogen bonds : angle 4.21859 ( 1281) metal coordination : bond 0.01143 ( 9) metal coordination : angle 1.54522 ( 3) covalent geometry : bond 0.00359 (12021) covalent geometry : angle 0.60895 (16875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6515 (m-10) REVERT: A 121 TYR cc_start: 0.8856 (t80) cc_final: 0.8302 (t80) REVERT: A 194 LEU cc_start: 0.9387 (mp) cc_final: 0.9175 (mp) REVERT: A 303 MET cc_start: 0.9125 (mmm) cc_final: 0.8909 (mmm) REVERT: A 346 ILE cc_start: 0.7048 (OUTLIER) cc_final: 0.6659 (mp) REVERT: A 448 MET cc_start: 0.8096 (ttp) cc_final: 0.7742 (ptm) REVERT: A 510 ASP cc_start: 0.8484 (m-30) cc_final: 0.8220 (m-30) REVERT: B 78 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7779 (t70) REVERT: B 292 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7328 (ppt90) REVERT: B 326 ASP cc_start: 0.8492 (t0) cc_final: 0.8174 (t0) REVERT: B 353 HIS cc_start: 0.8923 (t-90) cc_final: 0.8558 (t-170) outliers start: 26 outliers final: 17 residues processed: 74 average time/residue: 0.2323 time to fit residues: 25.7849 Evaluate side-chains 73 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 55 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.071556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052361 restraints weight = 62665.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.053790 restraints weight = 32515.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.054546 restraints weight = 21941.557| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12030 Z= 0.115 Angle : 0.586 12.966 16878 Z= 0.294 Chirality : 0.037 0.179 1944 Planarity : 0.004 0.041 1620 Dihedral : 21.005 169.546 3334 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.23 % Allowed : 21.16 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.27), residues: 1037 helix: 1.41 (0.25), residues: 463 sheet: -1.70 (0.44), residues: 138 loop : -2.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.008 0.001 HIS B 371 PHE 0.017 0.001 PHE A 214 TYR 0.011 0.001 TYR A 82 ARG 0.005 0.000 ARG B 34 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 479) hydrogen bonds : angle 4.06971 ( 1281) metal coordination : bond 0.00435 ( 9) metal coordination : angle 1.12332 ( 3) covalent geometry : bond 0.00243 (12021) covalent geometry : angle 0.58583 (16875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6359 (m-10) REVERT: A 121 TYR cc_start: 0.8817 (t80) cc_final: 0.8305 (t80) REVERT: A 194 LEU cc_start: 0.9405 (mp) cc_final: 0.9146 (mp) REVERT: A 309 ASP cc_start: 0.8695 (m-30) cc_final: 0.8484 (m-30) REVERT: A 346 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6544 (mp) REVERT: A 358 MET cc_start: 0.7975 (mtm) cc_final: 0.7493 (mtt) REVERT: A 448 MET cc_start: 0.7849 (ttp) cc_final: 0.7428 (ptm) REVERT: A 510 ASP cc_start: 0.8388 (m-30) cc_final: 0.8146 (m-30) REVERT: B 78 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7885 (t70) REVERT: B 292 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7260 (ppt90) REVERT: B 326 ASP cc_start: 0.8507 (t0) cc_final: 0.8219 (t0) REVERT: B 353 HIS cc_start: 0.8863 (t-90) cc_final: 0.8506 (t-170) REVERT: B 369 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7303 (p0) outliers start: 20 outliers final: 12 residues processed: 76 average time/residue: 0.2335 time to fit residues: 26.0963 Evaluate side-chains 71 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 390 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.068434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049250 restraints weight = 64026.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050610 restraints weight = 33547.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.051397 restraints weight = 22898.904| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12030 Z= 0.242 Angle : 0.683 14.460 16878 Z= 0.347 Chirality : 0.040 0.230 1944 Planarity : 0.004 0.046 1620 Dihedral : 21.147 168.164 3334 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.23 % Allowed : 21.94 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.27), residues: 1037 helix: 1.20 (0.24), residues: 466 sheet: -1.84 (0.43), residues: 142 loop : -2.22 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 223 HIS 0.011 0.002 HIS B 371 PHE 0.029 0.002 PHE A 214 TYR 0.015 0.002 TYR A 18 ARG 0.005 0.001 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 479) hydrogen bonds : angle 4.40185 ( 1281) metal coordination : bond 0.01718 ( 9) metal coordination : angle 2.00342 ( 3) covalent geometry : bond 0.00502 (12021) covalent geometry : angle 0.68281 (16875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.88 seconds wall clock time: 71 minutes 40.86 seconds (4300.86 seconds total)