Starting phenix.real_space_refine on Fri Aug 22 21:34:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo7_37681/08_2025/8wo7_37681.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5290 2.51 5 N 1306 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4031 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "B" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4031 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.31, per 1000 atoms: 0.28 Number of scatterers: 8118 At special positions: 0 Unit cell: (92.759, 105.524, 100.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1470 8.00 N 1306 7.00 C 5290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 463.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 67.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.459A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 117 through 149 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.315A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.895A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.594A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.058A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix removed outlier: 3.520A pdb=" N ILE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.540A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 554 removed outlier: 4.508A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.704A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 117 through 149 removed outlier: 3.570A pdb=" N CYS B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 180 through 201 removed outlier: 3.558A pdb=" N PHE B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.151A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.886A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.710A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 452 removed outlier: 4.282A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.524A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 501 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.806A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.610A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 241 through 242 507 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1258 1.31 - 1.44: 2240 1.44 - 1.57: 4723 1.57 - 1.69: 1 1.69 - 1.82: 84 Bond restraints: 8306 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.540 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.533 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.528 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.526 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" C7 NAG C 2 " pdb=" N2 NAG C 2 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 8301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10942 1.72 - 3.43: 286 3.43 - 5.15: 55 5.15 - 6.86: 20 6.86 - 8.58: 3 Bond angle restraints: 11306 Sorted by residual: angle pdb=" N LEU B 275 " pdb=" CA LEU B 275 " pdb=" C LEU B 275 " ideal model delta sigma weight residual 110.91 116.11 -5.20 1.17e+00 7.31e-01 1.97e+01 angle pdb=" N LEU A 275 " pdb=" CA LEU A 275 " pdb=" C LEU A 275 " ideal model delta sigma weight residual 110.91 115.84 -4.93 1.17e+00 7.31e-01 1.78e+01 angle pdb=" N SER A 274 " pdb=" CA SER A 274 " pdb=" C SER A 274 " ideal model delta sigma weight residual 109.94 116.25 -6.31 1.57e+00 4.06e-01 1.61e+01 angle pdb=" N SER B 274 " pdb=" CA SER B 274 " pdb=" C SER B 274 " ideal model delta sigma weight residual 109.94 116.15 -6.21 1.57e+00 4.06e-01 1.57e+01 angle pdb=" C THR A 247 " pdb=" N LEU A 248 " pdb=" CA LEU A 248 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 ... (remaining 11301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.82: 4651 22.82 - 45.64: 222 45.64 - 68.47: 22 68.47 - 91.29: 2 91.29 - 114.11: 3 Dihedral angle restraints: 4900 sinusoidal: 1846 harmonic: 3054 Sorted by residual: dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 142.36 37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CB CYS A 254 " pdb=" SG CYS A 254 " pdb=" SG CYS A 287 " pdb=" CB CYS A 287 " ideal model delta sinusoidal sigma weight residual 93.00 157.27 -64.27 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB CYS B 254 " pdb=" SG CYS B 254 " pdb=" SG CYS B 287 " pdb=" CB CYS B 287 " ideal model delta sinusoidal sigma weight residual 93.00 157.00 -64.00 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 4897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1075 0.052 - 0.105: 239 0.105 - 0.157: 32 0.157 - 0.210: 5 0.210 - 0.262: 3 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C5 NAG C 1 " pdb=" C4 NAG C 1 " pdb=" C6 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.67 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C5 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" C6 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1351 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 248 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LEU A 248 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU A 248 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 249 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 487 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 487 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 118 2.67 - 3.22: 8314 3.22 - 3.78: 13371 3.78 - 4.34: 18337 4.34 - 4.90: 30079 Nonbonded interactions: 70219 Sorted by model distance: nonbonded pdb=" OG1 THR A 162 " pdb=" OH TYR A 440 " model vdw 2.107 3.040 nonbonded pdb=" O VAL A 539 " pdb=" OH TYR B 309 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASP B 390 " pdb=" OH TYR B 440 " model vdw 2.155 3.040 nonbonded pdb=" OH TYR A 309 " pdb=" O VAL B 539 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU A 49 " pdb=" OG1 THR A 455 " model vdw 2.210 3.040 ... (remaining 70214 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.250 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.007 0.127 8318 Z= 0.337 Angle : 0.699 8.581 11334 Z= 0.368 Chirality : 0.045 0.262 1354 Planarity : 0.005 0.074 1398 Dihedral : 13.009 114.111 2936 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1076 helix: 1.66 (0.20), residues: 640 sheet: -4.54 (0.75), residues: 20 loop : -0.14 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 32 TYR 0.018 0.001 TYR A 524 PHE 0.026 0.002 PHE B 442 TRP 0.006 0.001 TRP B 380 HIS 0.003 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00714 ( 8306) covalent geometry : angle 0.69066 (11306) SS BOND : bond 0.00357 ( 8) SS BOND : angle 2.32033 ( 16) hydrogen bonds : bond 0.16925 ( 507) hydrogen bonds : angle 6.10786 ( 1434) link_BETA1-4 : bond 0.00757 ( 2) link_BETA1-4 : angle 2.38553 ( 6) link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 1.86611 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.298 Fit side-chains REVERT: A 23 ARG cc_start: 0.7331 (mtp-110) cc_final: 0.6392 (tmt170) REVERT: A 356 ILE cc_start: 0.9056 (mm) cc_final: 0.8814 (mt) REVERT: A 451 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7906 (mp0) REVERT: B 23 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7135 (tmt170) REVERT: B 139 SER cc_start: 0.8692 (m) cc_final: 0.8457 (m) REVERT: B 356 ILE cc_start: 0.9089 (mm) cc_final: 0.8852 (mt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.5463 time to fit residues: 80.2744 Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119594 restraints weight = 10017.177| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.21 r_work: 0.3312 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8318 Z= 0.139 Angle : 0.598 9.555 11334 Z= 0.307 Chirality : 0.041 0.176 1354 Planarity : 0.005 0.073 1398 Dihedral : 7.483 92.567 1232 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 1.75 % Allowed : 8.62 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.26), residues: 1076 helix: 1.96 (0.20), residues: 646 sheet: -4.50 (0.74), residues: 20 loop : -0.25 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.022 0.002 TYR A 440 PHE 0.020 0.001 PHE B 195 TRP 0.010 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8306) covalent geometry : angle 0.58715 (11306) SS BOND : bond 0.00129 ( 8) SS BOND : angle 1.33628 ( 16) hydrogen bonds : bond 0.04532 ( 507) hydrogen bonds : angle 4.76293 ( 1434) link_BETA1-4 : bond 0.00756 ( 2) link_BETA1-4 : angle 3.96052 ( 6) link_NAG-ASN : bond 0.00203 ( 2) link_NAG-ASN : angle 2.38824 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.300 Fit side-chains REVERT: A 23 ARG cc_start: 0.7374 (mtp-110) cc_final: 0.6286 (tmt170) REVERT: A 451 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8037 (mp0) REVERT: B 23 ARG cc_start: 0.7940 (mtp85) cc_final: 0.6858 (tmt170) REVERT: B 235 ASN cc_start: 0.8586 (p0) cc_final: 0.8252 (p0) REVERT: B 548 GLU cc_start: 0.7531 (tp30) cc_final: 0.7272 (mm-30) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.5013 time to fit residues: 68.5581 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 497 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121291 restraints weight = 9893.278| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.19 r_work: 0.3324 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8318 Z= 0.127 Angle : 0.570 10.682 11334 Z= 0.288 Chirality : 0.041 0.199 1354 Planarity : 0.005 0.074 1398 Dihedral : 6.797 79.992 1232 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 12.12 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.26), residues: 1076 helix: 2.07 (0.20), residues: 644 sheet: -4.48 (0.74), residues: 20 loop : -0.22 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 36 TYR 0.021 0.001 TYR A 440 PHE 0.016 0.001 PHE B 166 TRP 0.010 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8306) covalent geometry : angle 0.55731 (11306) SS BOND : bond 0.00175 ( 8) SS BOND : angle 1.11456 ( 16) hydrogen bonds : bond 0.04014 ( 507) hydrogen bonds : angle 4.52653 ( 1434) link_BETA1-4 : bond 0.00599 ( 2) link_BETA1-4 : angle 4.32311 ( 6) link_NAG-ASN : bond 0.00044 ( 2) link_NAG-ASN : angle 2.34816 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.313 Fit side-chains REVERT: A 23 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6334 (tmt170) REVERT: A 321 TYR cc_start: 0.8472 (m-10) cc_final: 0.7619 (m-10) REVERT: A 451 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8332 (tp30) REVERT: B 23 ARG cc_start: 0.7843 (mtp85) cc_final: 0.6851 (tmt170) REVERT: B 496 MET cc_start: 0.8935 (tpt) cc_final: 0.8690 (tpt) outliers start: 17 outliers final: 6 residues processed: 124 average time/residue: 0.5083 time to fit residues: 67.3128 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 374 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120599 restraints weight = 10084.858| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.18 r_work: 0.3317 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8318 Z= 0.130 Angle : 0.574 11.279 11334 Z= 0.289 Chirality : 0.041 0.188 1354 Planarity : 0.005 0.074 1398 Dihedral : 6.129 63.771 1232 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.33 % Allowed : 13.87 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.26), residues: 1076 helix: 2.17 (0.20), residues: 644 sheet: -4.47 (0.75), residues: 20 loop : -0.20 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.019 0.001 TYR A 440 PHE 0.016 0.001 PHE B 166 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8306) covalent geometry : angle 0.55988 (11306) SS BOND : bond 0.00181 ( 8) SS BOND : angle 1.08377 ( 16) hydrogen bonds : bond 0.03750 ( 507) hydrogen bonds : angle 4.41655 ( 1434) link_BETA1-4 : bond 0.00436 ( 2) link_BETA1-4 : angle 4.87864 ( 6) link_NAG-ASN : bond 0.00043 ( 2) link_NAG-ASN : angle 2.27730 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.6318 (tmt170) REVERT: A 195 PHE cc_start: 0.7909 (m-10) cc_final: 0.7698 (m-10) REVERT: A 321 TYR cc_start: 0.8429 (m-10) cc_final: 0.7621 (m-10) REVERT: A 451 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8283 (tp30) REVERT: B 23 ARG cc_start: 0.7786 (mtp85) cc_final: 0.6814 (tmt170) REVERT: B 319 MET cc_start: 0.8439 (mmt) cc_final: 0.8223 (mmm) REVERT: B 320 ILE cc_start: 0.8075 (mp) cc_final: 0.7815 (tp) outliers start: 20 outliers final: 7 residues processed: 123 average time/residue: 0.4800 time to fit residues: 63.5974 Evaluate side-chains 98 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 67 ASN B 163 ASN B 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118520 restraints weight = 10098.856| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.17 r_work: 0.3303 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8318 Z= 0.131 Angle : 0.578 11.072 11334 Z= 0.287 Chirality : 0.041 0.189 1354 Planarity : 0.005 0.074 1398 Dihedral : 5.356 39.447 1232 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.45 % Allowed : 15.38 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.26), residues: 1076 helix: 2.22 (0.20), residues: 644 sheet: -4.44 (0.76), residues: 20 loop : -0.17 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.020 0.001 TYR A 440 PHE 0.016 0.001 PHE A 166 TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8306) covalent geometry : angle 0.56013 (11306) SS BOND : bond 0.00178 ( 8) SS BOND : angle 1.16240 ( 16) hydrogen bonds : bond 0.03629 ( 507) hydrogen bonds : angle 4.34778 ( 1434) link_BETA1-4 : bond 0.00384 ( 2) link_BETA1-4 : angle 5.53356 ( 6) link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 2.34056 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6351 (tmt170) REVERT: A 195 PHE cc_start: 0.7905 (m-10) cc_final: 0.7693 (m-10) REVERT: A 321 TYR cc_start: 0.8413 (m-10) cc_final: 0.7646 (m-10) REVERT: A 451 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8343 (tp30) REVERT: B 23 ARG cc_start: 0.7764 (mtp85) cc_final: 0.6891 (tmt170) REVERT: B 319 MET cc_start: 0.8471 (mmt) cc_final: 0.8163 (mmm) outliers start: 21 outliers final: 12 residues processed: 112 average time/residue: 0.4839 time to fit residues: 58.5234 Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.147562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119161 restraints weight = 10042.788| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.18 r_work: 0.3313 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8318 Z= 0.119 Angle : 0.547 12.010 11334 Z= 0.276 Chirality : 0.041 0.153 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.896 34.965 1232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.15 % Allowed : 15.50 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.26), residues: 1076 helix: 2.32 (0.20), residues: 646 sheet: -4.43 (0.74), residues: 20 loop : -0.09 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.017 0.001 TYR A 440 PHE 0.015 0.001 PHE B 166 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8306) covalent geometry : angle 0.52840 (11306) SS BOND : bond 0.00174 ( 8) SS BOND : angle 1.10566 ( 16) hydrogen bonds : bond 0.03500 ( 507) hydrogen bonds : angle 4.29957 ( 1434) link_BETA1-4 : bond 0.00314 ( 2) link_BETA1-4 : angle 5.50507 ( 6) link_NAG-ASN : bond 0.00142 ( 2) link_NAG-ASN : angle 2.44726 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7357 (mtp-110) cc_final: 0.6350 (tmt170) REVERT: B 23 ARG cc_start: 0.7687 (mtp85) cc_final: 0.6793 (tmt170) REVERT: B 319 MET cc_start: 0.8565 (mmt) cc_final: 0.8311 (mmm) REVERT: B 321 TYR cc_start: 0.8431 (m-10) cc_final: 0.7626 (m-10) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 0.4475 time to fit residues: 57.1939 Evaluate side-chains 110 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 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 = 0.3760 r_free = 0.3760 target = 0.147055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118644 restraints weight = 10182.385| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.18 r_work: 0.3311 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8318 Z= 0.129 Angle : 0.557 11.244 11334 Z= 0.283 Chirality : 0.042 0.205 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.854 35.291 1232 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.21 % Allowed : 17.37 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.26), residues: 1076 helix: 2.33 (0.20), residues: 644 sheet: -4.44 (0.77), residues: 20 loop : -0.08 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.018 0.001 TYR A 440 PHE 0.016 0.001 PHE B 166 TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8306) covalent geometry : angle 0.54017 (11306) SS BOND : bond 0.00186 ( 8) SS BOND : angle 1.23756 ( 16) hydrogen bonds : bond 0.03524 ( 507) hydrogen bonds : angle 4.30234 ( 1434) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 5.11747 ( 6) link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 2.45021 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6372 (tmt170) REVERT: A 195 PHE cc_start: 0.7872 (m-10) cc_final: 0.7655 (m-10) REVERT: B 23 ARG cc_start: 0.7631 (mtp85) cc_final: 0.6728 (tmt170) REVERT: B 319 MET cc_start: 0.8610 (mmt) cc_final: 0.8358 (mmm) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.4867 time to fit residues: 55.8136 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119648 restraints weight = 10047.377| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.18 r_work: 0.3319 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8318 Z= 0.118 Angle : 0.541 10.635 11334 Z= 0.277 Chirality : 0.041 0.164 1354 Planarity : 0.005 0.076 1398 Dihedral : 4.725 34.951 1232 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 2.21 % Allowed : 17.13 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.26), residues: 1076 helix: 2.37 (0.20), residues: 646 sheet: -4.44 (0.75), residues: 20 loop : -0.07 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.017 0.001 TYR A 440 PHE 0.015 0.001 PHE B 166 TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8306) covalent geometry : angle 0.52599 (11306) SS BOND : bond 0.00251 ( 8) SS BOND : angle 1.00523 ( 16) hydrogen bonds : bond 0.03418 ( 507) hydrogen bonds : angle 4.28350 ( 1434) link_BETA1-4 : bond 0.00264 ( 2) link_BETA1-4 : angle 4.85107 ( 6) link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 2.41156 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.307 Fit side-chains REVERT: A 23 ARG cc_start: 0.7336 (mtp-110) cc_final: 0.6332 (tmt170) REVERT: A 195 PHE cc_start: 0.7874 (m-10) cc_final: 0.7649 (m-10) REVERT: A 235 ASN cc_start: 0.8450 (p0) cc_final: 0.8171 (p0) REVERT: A 321 TYR cc_start: 0.8362 (m-10) cc_final: 0.7628 (m-10) REVERT: B 23 ARG cc_start: 0.7660 (mtp85) cc_final: 0.6729 (tmt170) REVERT: B 35 LYS cc_start: 0.8405 (mttp) cc_final: 0.8004 (mmtp) REVERT: B 123 CYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5753 (t) REVERT: B 319 MET cc_start: 0.8612 (mmt) cc_final: 0.8341 (mmm) outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 0.4864 time to fit residues: 56.0742 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120500 restraints weight = 10128.587| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.19 r_work: 0.3334 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8318 Z= 0.113 Angle : 0.541 10.060 11334 Z= 0.275 Chirality : 0.041 0.180 1354 Planarity : 0.005 0.076 1398 Dihedral : 4.622 34.969 1232 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 2.56 % Allowed : 16.78 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.26), residues: 1076 helix: 2.39 (0.20), residues: 646 sheet: -4.39 (0.78), residues: 20 loop : -0.01 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.017 0.001 TYR A 440 PHE 0.014 0.001 PHE B 166 TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8306) covalent geometry : angle 0.52682 (11306) SS BOND : bond 0.00264 ( 8) SS BOND : angle 0.99441 ( 16) hydrogen bonds : bond 0.03341 ( 507) hydrogen bonds : angle 4.25409 ( 1434) link_BETA1-4 : bond 0.00333 ( 2) link_BETA1-4 : angle 4.60244 ( 6) link_NAG-ASN : bond 0.00145 ( 2) link_NAG-ASN : angle 2.39681 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.240 Fit side-chains REVERT: A 23 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6334 (tmt170) REVERT: A 235 ASN cc_start: 0.8350 (p0) cc_final: 0.8109 (p0) REVERT: A 293 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 321 TYR cc_start: 0.8346 (m-10) cc_final: 0.7678 (m-10) REVERT: B 23 ARG cc_start: 0.7652 (mtp85) cc_final: 0.6734 (tmt170) REVERT: B 35 LYS cc_start: 0.8386 (mttp) cc_final: 0.8068 (mmtp) REVERT: B 319 MET cc_start: 0.8561 (mmt) cc_final: 0.8277 (mmm) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 0.4707 time to fit residues: 55.2942 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 470 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121366 restraints weight = 10143.798| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.21 r_work: 0.3348 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8318 Z= 0.110 Angle : 0.541 9.647 11334 Z= 0.277 Chirality : 0.041 0.173 1354 Planarity : 0.005 0.077 1398 Dihedral : 4.556 34.941 1232 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.40 % Allowed : 18.07 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.26), residues: 1076 helix: 2.40 (0.20), residues: 646 sheet: -4.40 (0.77), residues: 20 loop : -0.03 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.018 0.001 TYR A 440 PHE 0.014 0.001 PHE B 166 TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8306) covalent geometry : angle 0.52310 (11306) SS BOND : bond 0.00279 ( 8) SS BOND : angle 2.03333 ( 16) hydrogen bonds : bond 0.03278 ( 507) hydrogen bonds : angle 4.25584 ( 1434) link_BETA1-4 : bond 0.00380 ( 2) link_BETA1-4 : angle 4.45609 ( 6) link_NAG-ASN : bond 0.00153 ( 2) link_NAG-ASN : angle 2.40656 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.189 Fit side-chains REVERT: A 23 ARG cc_start: 0.7297 (mtp-110) cc_final: 0.6304 (tmt170) REVERT: A 293 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 23 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6713 (tmt170) REVERT: B 35 LYS cc_start: 0.8386 (mttp) cc_final: 0.8070 (mmtp) REVERT: B 293 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8367 (mt-10) REVERT: B 319 MET cc_start: 0.8584 (mmt) cc_final: 0.8296 (mmm) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.4779 time to fit residues: 55.4520 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 440 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120327 restraints weight = 10140.571| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.20 r_work: 0.3334 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8318 Z= 0.125 Angle : 0.558 9.737 11334 Z= 0.285 Chirality : 0.041 0.177 1354 Planarity : 0.005 0.076 1398 Dihedral : 4.579 35.217 1232 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.40 % Allowed : 18.30 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.26), residues: 1076 helix: 2.38 (0.20), residues: 646 sheet: -4.41 (0.77), residues: 20 loop : -0.07 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.018 0.001 TYR A 440 PHE 0.015 0.001 PHE B 166 TRP 0.008 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8306) covalent geometry : angle 0.53643 (11306) SS BOND : bond 0.00764 ( 8) SS BOND : angle 2.84730 ( 16) hydrogen bonds : bond 0.03332 ( 507) hydrogen bonds : angle 4.28509 ( 1434) link_BETA1-4 : bond 0.00432 ( 2) link_BETA1-4 : angle 4.27777 ( 6) link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 2.52699 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.60 seconds wall clock time: 47 minutes 48.18 seconds (2868.18 seconds total)