Starting phenix.real_space_refine on Wed Mar 12 16:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo7_37681/03_2025/8wo7_37681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo7_37681/03_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_37681/03_2025/8wo7_37681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo7_37681/03_2025/8wo7_37681.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo7_37681/03_2025/8wo7_37681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo7_37681/03_2025/8wo7_37681.cif" } resolution = 2.9 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.29, per 1000 atoms: 0.65 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: 2.17 Conformation dependent library (CDL) restraints added in 988.5 milliseconds 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: 0.77 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: 2.42 Time building geometry restraints manager: 2.55 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: 0.00 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: 92.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.920 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:59.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.380 ------------------------------------------------------------------------------- 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 8306 Z= 0.467 Angle : 0.691 8.581 11306 Z= 0.365 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 : 7.94 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 (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: 1.23 (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 TRP 0.006 0.001 TRP B 380 HIS 0.003 0.001 HIS B 364 PHE 0.026 0.002 PHE B 442 TYR 0.018 0.001 TYR A 524 ARG 0.002 0.000 ARG A 32 *********************** 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 : 0.827 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: 1.0630 time to fit residues: 156.8046 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 : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 98 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.149308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120720 restraints weight = 9886.378| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.19 r_work: 0.3317 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8306 Z= 0.204 Angle : 0.589 9.344 11306 Z= 0.306 Chirality : 0.041 0.169 1354 Planarity : 0.005 0.073 1398 Dihedral : 7.549 93.724 1232 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 8.74 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.48 (0.26), residues: 1076 helix: 1.95 (0.20), residues: 646 sheet: -4.51 (0.74), residues: 20 loop : -0.25 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 PHE 0.018 0.001 PHE B 195 TYR 0.022 0.002 TYR A 440 ARG 0.003 0.000 ARG A 36 *********************** 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 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.952 Fit side-chains REVERT: A 23 ARG cc_start: 0.7342 (mtp-110) cc_final: 0.6296 (tmt170) REVERT: A 451 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8005 (mp0) REVERT: B 23 ARG cc_start: 0.7929 (mtp85) cc_final: 0.6835 (tmt170) REVERT: B 235 ASN cc_start: 0.8580 (p0) cc_final: 0.8230 (p0) REVERT: B 548 GLU cc_start: 0.7497 (tp30) cc_final: 0.7234 (mm-30) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 1.0841 time to fit residues: 146.5560 Evaluate side-chains 102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.147327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118650 restraints weight = 10100.838| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.19 r_work: 0.3288 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8306 Z= 0.257 Angle : 0.583 10.582 11306 Z= 0.297 Chirality : 0.042 0.210 1354 Planarity : 0.005 0.072 1398 Dihedral : 6.906 81.591 1232 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 12.59 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.53 (0.26), residues: 1076 helix: 2.02 (0.20), residues: 644 sheet: -4.51 (0.74), residues: 20 loop : -0.28 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS B 364 PHE 0.017 0.001 PHE B 166 TYR 0.022 0.002 TYR A 440 ARG 0.003 0.000 ARG A 36 *********************** 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 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.905 Fit side-chains REVERT: A 23 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6352 (tmt170) REVERT: B 23 ARG cc_start: 0.7873 (mtp85) cc_final: 0.6866 (tmt170) REVERT: B 451 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8245 (mp0) outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.9983 time to fit residues: 125.6314 Evaluate side-chains 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 470 MET Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 451 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 350 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116527 restraints weight = 10021.710| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.18 r_work: 0.3275 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8306 Z= 0.270 Angle : 0.586 11.194 11306 Z= 0.298 Chirality : 0.042 0.215 1354 Planarity : 0.005 0.070 1398 Dihedral : 6.277 65.227 1232 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.21 % Allowed : 13.40 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1076 helix: 1.92 (0.20), residues: 656 sheet: -4.49 (0.76), residues: 20 loop : -0.41 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.001 HIS B 364 PHE 0.018 0.001 PHE B 166 TYR 0.020 0.001 TYR A 440 ARG 0.002 0.000 ARG A 36 *********************** 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 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6330 (tmt170) REVERT: B 23 ARG cc_start: 0.7838 (mtp85) cc_final: 0.6845 (tmt170) REVERT: B 319 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8334 (mmm) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 0.9842 time to fit residues: 123.0590 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 470 MET 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 319 MET Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 0.0470 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 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 = 0.3780 r_free = 0.3780 target = 0.148732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120555 restraints weight = 9913.961| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.14 r_work: 0.3312 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8306 Z= 0.175 Angle : 0.553 9.815 11306 Z= 0.279 Chirality : 0.041 0.190 1354 Planarity : 0.005 0.073 1398 Dihedral : 5.365 38.152 1232 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.68 % Allowed : 14.57 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.78 (0.26), residues: 1076 helix: 2.20 (0.20), residues: 646 sheet: -4.40 (0.78), residues: 20 loop : -0.14 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.001 0.000 HIS B 350 PHE 0.015 0.001 PHE B 166 TYR 0.018 0.001 TYR A 440 ARG 0.002 0.000 ARG A 36 *********************** 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 131 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.6350 (tmt170) REVERT: A 321 TYR cc_start: 0.8446 (m-10) cc_final: 0.7663 (m-10) REVERT: B 23 ARG cc_start: 0.7756 (mtp85) cc_final: 0.6871 (tmt170) REVERT: B 321 TYR cc_start: 0.8463 (m-10) cc_final: 0.7656 (m-10) outliers start: 23 outliers final: 11 residues processed: 122 average time/residue: 0.9028 time to fit residues: 119.6614 Evaluate side-chains 104 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 374 ILE 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 374 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.145607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117194 restraints weight = 9996.826| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.16 r_work: 0.3284 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8306 Z= 0.220 Angle : 0.547 9.890 11306 Z= 0.282 Chirality : 0.042 0.181 1354 Planarity : 0.005 0.073 1398 Dihedral : 4.998 35.403 1232 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.03 % Allowed : 15.73 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.83 (0.26), residues: 1076 helix: 2.25 (0.20), residues: 644 sheet: -4.41 (0.78), residues: 20 loop : -0.14 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 PHE 0.016 0.001 PHE B 166 TYR 0.018 0.001 TYR A 440 ARG 0.001 0.000 ARG A 36 *********************** 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 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7374 (mtp-110) cc_final: 0.6355 (tmt170) REVERT: A 518 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8593 (tt) REVERT: B 23 ARG cc_start: 0.7754 (mtp85) cc_final: 0.6863 (tmt170) outliers start: 26 outliers final: 12 residues processed: 110 average time/residue: 0.9332 time to fit residues: 111.2251 Evaluate side-chains 105 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 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 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119812 restraints weight = 9969.248| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.14 r_work: 0.3306 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8306 Z= 0.194 Angle : 0.533 9.374 11306 Z= 0.276 Chirality : 0.041 0.185 1354 Planarity : 0.005 0.074 1398 Dihedral : 4.915 35.461 1232 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.80 % Allowed : 16.55 % 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 (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: 1.87 (0.26), residues: 1076 helix: 2.27 (0.20), residues: 646 sheet: -4.47 (0.75), residues: 20 loop : -0.08 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 364 PHE 0.015 0.001 PHE B 166 TYR 0.018 0.001 TYR A 440 ARG 0.002 0.000 ARG B 204 *********************** 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 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6368 (tmt170) REVERT: A 518 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (tt) REVERT: B 23 ARG cc_start: 0.7723 (mtp85) cc_final: 0.6813 (tmt170) REVERT: B 321 TYR cc_start: 0.8409 (m-10) cc_final: 0.7631 (m-10) outliers start: 24 outliers final: 14 residues processed: 115 average time/residue: 0.9555 time to fit residues: 119.0535 Evaluate side-chains 111 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 507 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 201 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 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 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 = 0.147053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118844 restraints weight = 10116.059| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.17 r_work: 0.3306 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8306 Z= 0.189 Angle : 0.537 10.193 11306 Z= 0.275 Chirality : 0.041 0.162 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.811 34.943 1232 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 2.45 % Allowed : 16.78 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1076 helix: 2.30 (0.20), residues: 646 sheet: -4.40 (0.75), residues: 20 loop : -0.06 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS A 364 PHE 0.015 0.001 PHE B 166 TYR 0.016 0.001 TYR A 440 ARG 0.004 0.000 ARG B 103 *********************** 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 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7352 (mtp-110) cc_final: 0.6339 (tmt170) REVERT: A 235 ASN cc_start: 0.8481 (p0) cc_final: 0.8141 (p0) REVERT: B 23 ARG cc_start: 0.7670 (mtp85) cc_final: 0.6786 (tmt170) REVERT: B 321 TYR cc_start: 0.8392 (m-10) cc_final: 0.7615 (m-10) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.9956 time to fit residues: 117.0502 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 507 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 440 TYR Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.144305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115844 restraints weight = 10249.588| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.16 r_work: 0.3247 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8306 Z= 0.307 Angle : 0.579 9.377 11306 Z= 0.299 Chirality : 0.043 0.237 1354 Planarity : 0.005 0.072 1398 Dihedral : 4.985 36.159 1232 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.90 % Favored : 95.91 % Rotamer: Outliers : 2.68 % Allowed : 16.67 % 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 (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: 1.85 (0.26), residues: 1076 helix: 2.22 (0.20), residues: 642 sheet: -4.44 (0.78), residues: 20 loop : -0.00 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.002 0.001 HIS B 364 PHE 0.019 0.001 PHE A 166 TYR 0.019 0.002 TYR A 440 ARG 0.004 0.000 ARG B 36 *********************** 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 117 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7383 (mtp-110) cc_final: 0.6340 (tmt170) REVERT: A 235 ASN cc_start: 0.8556 (p0) cc_final: 0.8203 (p0) REVERT: A 468 LEU cc_start: 0.8526 (mm) cc_final: 0.8272 (mt) REVERT: B 23 ARG cc_start: 0.7775 (mtp85) cc_final: 0.6884 (tmt170) outliers start: 23 outliers final: 11 residues processed: 107 average time/residue: 1.0204 time to fit residues: 117.5427 Evaluate side-chains 102 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 A residue 507 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 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.0670 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 chunk 97 optimal weight: 5.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120682 restraints weight = 10039.334| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.15 r_work: 0.3331 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8306 Z= 0.157 Angle : 0.533 9.988 11306 Z= 0.274 Chirality : 0.040 0.178 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.766 34.210 1232 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 18.65 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1076 helix: 2.34 (0.20), residues: 646 sheet: -4.36 (0.76), residues: 20 loop : -0.01 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 482 HIS 0.002 0.000 HIS A 364 PHE 0.013 0.001 PHE A 166 TYR 0.017 0.001 TYR A 440 ARG 0.004 0.000 ARG B 36 ********************** 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 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7293 (mtp-110) cc_final: 0.6277 (tmt170) REVERT: A 235 ASN cc_start: 0.8353 (p0) cc_final: 0.8100 (p0) REVERT: A 293 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8441 (mt-10) REVERT: A 321 TYR cc_start: 0.8338 (m-10) cc_final: 0.7611 (m-10) REVERT: B 23 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6750 (tmt170) REVERT: B 321 TYR cc_start: 0.8359 (m-10) cc_final: 0.7620 (m-10) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.9786 time to fit residues: 115.1649 Evaluate side-chains 101 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 440 TYR Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 35 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 0.0370 chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.5470 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120330 restraints weight = 10136.446| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.18 r_work: 0.3332 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8306 Z= 0.170 Angle : 0.523 7.854 11306 Z= 0.271 Chirality : 0.041 0.187 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.657 34.833 1232 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.88 % Favored : 96.93 % 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 (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: 2.04 (0.26), residues: 1076 helix: 2.38 (0.20), residues: 646 sheet: -4.46 (0.74), residues: 20 loop : 0.02 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 482 HIS 0.001 0.000 HIS A 364 PHE 0.015 0.001 PHE B 166 TYR 0.016 0.001 TYR A 440 ARG 0.004 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5655.37 seconds wall clock time: 98 minutes 1.71 seconds (5881.71 seconds total)