Starting phenix.real_space_refine on Sun May 11 13:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wo7_37681/05_2025/8wo7_37681.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wo7_37681/05_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_37681/05_2025/8wo7_37681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wo7_37681/05_2025/8wo7_37681.map" model { file = "/net/cci-nas-00/data/ceres_data/8wo7_37681/05_2025/8wo7_37681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wo7_37681/05_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-5687/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: 5.05, per 1000 atoms: 0.62 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: 2.25 Conformation dependent library (CDL) restraints added in 972.8 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: 0.86 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: 2.23 Time building geometry restraints manager: 2.58 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: 3.880 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.640 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 1.86611 ( 6) link_BETA1-4 : bond 0.00757 ( 2) link_BETA1-4 : angle 2.38553 ( 6) hydrogen bonds : bond 0.16925 ( 507) hydrogen bonds : angle 6.10786 ( 1434) SS BOND : bond 0.00357 ( 8) SS BOND : angle 2.32033 ( 16) covalent geometry : bond 0.00714 ( 8306) covalent geometry : angle 0.69066 (11306) *********************** 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 : 0.918 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: 1.0955 time to fit residues: 161.6980 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 : 0.899 ------------------------------------------------------------------------------- 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 = 0.149304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120719 restraints weight = 9886.053| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.19 r_work: 0.3316 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 8318 Z= 0.138 Angle : 0.600 9.348 11334 Z= 0.309 Chirality : 0.041 0.169 1354 Planarity : 0.005 0.073 1398 Dihedral : 7.546 93.675 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: 1.96 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 2) link_NAG-ASN : angle 2.47297 ( 6) link_BETA1-4 : bond 0.00510 ( 2) link_BETA1-4 : angle 3.93431 ( 6) hydrogen bonds : bond 0.04581 ( 507) hydrogen bonds : angle 4.77354 ( 1434) SS BOND : bond 0.00118 ( 8) SS BOND : angle 1.32436 ( 16) covalent geometry : bond 0.00306 ( 8306) covalent geometry : angle 0.58865 (11306) *********************** 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 : 0.781 Fit side-chains REVERT: A 23 ARG cc_start: 0.7339 (mtp-110) cc_final: 0.6293 (tmt170) REVERT: A 451 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8003 (mp0) REVERT: B 23 ARG cc_start: 0.7928 (mtp85) cc_final: 0.6832 (tmt170) REVERT: B 235 ASN cc_start: 0.8583 (p0) cc_final: 0.8231 (p0) REVERT: B 548 GLU cc_start: 0.7484 (tp30) cc_final: 0.7222 (mm-30) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 1.0351 time to fit residues: 139.8109 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 : 0.826 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.146280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117557 restraints weight = 10112.735| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.19 r_work: 0.3274 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8318 Z= 0.180 Angle : 0.606 10.557 11334 Z= 0.305 Chirality : 0.042 0.216 1354 Planarity : 0.005 0.071 1398 Dihedral : 6.909 81.197 1232 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.21 % Allowed : 12.35 % Favored : 85.43 % 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: 1.49 (0.26), residues: 1076 helix: 1.99 (0.20), residues: 644 sheet: -4.52 (0.73), residues: 20 loop : -0.30 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.003 0.001 HIS B 364 PHE 0.018 0.002 PHE B 166 TYR 0.022 0.002 TYR A 440 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 2.59040 ( 6) link_BETA1-4 : bond 0.00564 ( 2) link_BETA1-4 : angle 4.25787 ( 6) hydrogen bonds : bond 0.04239 ( 507) hydrogen bonds : angle 4.55476 ( 1434) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.58386 ( 16) covalent geometry : bond 0.00432 ( 8306) covalent geometry : angle 0.59252 (11306) *********************** 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: 19 poor density : 106 time to evaluate : 0.978 Fit side-chains REVERT: A 23 ARG cc_start: 0.7378 (mtp-110) cc_final: 0.6352 (tmt170) REVERT: A 250 THR cc_start: 0.8618 (p) cc_final: 0.8413 (p) REVERT: A 319 MET cc_start: 0.8702 (mmt) cc_final: 0.8486 (mmm) REVERT: A 356 ILE cc_start: 0.9169 (mm) cc_final: 0.8898 (mt) REVERT: B 23 ARG cc_start: 0.7880 (mtp85) cc_final: 0.6873 (tmt170) REVERT: B 356 ILE cc_start: 0.9168 (mm) cc_final: 0.8906 (mt) REVERT: B 451 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (mp0) outliers start: 19 outliers final: 7 residues processed: 117 average time/residue: 0.9600 time to fit residues: 121.4059 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117634 restraints weight = 9977.798| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.18 r_work: 0.3292 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8318 Z= 0.140 Angle : 0.589 11.217 11334 Z= 0.294 Chirality : 0.041 0.177 1354 Planarity : 0.005 0.072 1398 Dihedral : 6.294 67.090 1232 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.98 % Allowed : 13.87 % Favored : 84.15 % 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: 1.62 (0.26), residues: 1076 helix: 2.10 (0.20), residues: 644 sheet: -4.54 (0.72), residues: 20 loop : -0.25 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 0.000 HIS B 364 PHE 0.016 0.001 PHE B 166 TYR 0.019 0.001 TYR A 440 ARG 0.002 0.000 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 2.32500 ( 6) link_BETA1-4 : bond 0.00527 ( 2) link_BETA1-4 : angle 4.77019 ( 6) hydrogen bonds : bond 0.03852 ( 507) hydrogen bonds : angle 4.45170 ( 1434) SS BOND : bond 0.00474 ( 8) SS BOND : angle 1.06329 ( 16) covalent geometry : bond 0.00329 ( 8306) covalent geometry : angle 0.57563 (11306) *********************** 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: 17 poor density : 109 time to evaluate : 0.844 Fit side-chains REVERT: A 23 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6338 (tmt170) REVERT: B 23 ARG cc_start: 0.7825 (mtp85) cc_final: 0.6834 (tmt170) REVERT: B 319 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8289 (mmm) REVERT: B 451 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8180 (mp0) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.9685 time to fit residues: 121.1131 Evaluate side-chains 100 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 374 ILE Chi-restraints excluded: chain A residue 518 ILE 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 451 GLU 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: 0.5980 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 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 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 = 0.3759 r_free = 0.3759 target = 0.147003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118797 restraints weight = 9958.787| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8318 Z= 0.125 Angle : 0.570 10.951 11334 Z= 0.285 Chirality : 0.041 0.208 1354 Planarity : 0.005 0.073 1398 Dihedral : 5.393 40.295 1232 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: 1.82 (0.26), residues: 1076 helix: 2.24 (0.20), residues: 644 sheet: -4.40 (0.79), residues: 20 loop : -0.13 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.002 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 2.31165 ( 6) link_BETA1-4 : bond 0.00346 ( 2) link_BETA1-4 : angle 5.49528 ( 6) hydrogen bonds : bond 0.03644 ( 507) hydrogen bonds : angle 4.35621 ( 1434) SS BOND : bond 0.00322 ( 8) SS BOND : angle 0.99070 ( 16) covalent geometry : bond 0.00287 ( 8306) covalent geometry : angle 0.55236 (11306) *********************** 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 127 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.838 Fit side-chains REVERT: A 23 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.6346 (tmt170) REVERT: A 321 TYR cc_start: 0.8438 (m-10) cc_final: 0.7650 (m-10) REVERT: B 23 ARG cc_start: 0.7780 (mtp85) cc_final: 0.6874 (tmt170) REVERT: B 59 THR cc_start: 0.8602 (m) cc_final: 0.8371 (p) REVERT: B 321 TYR cc_start: 0.8451 (m-10) cc_final: 0.7637 (m-10) outliers start: 23 outliers final: 9 residues processed: 118 average time/residue: 0.8959 time to fit residues: 114.5180 Evaluate side-chains 103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 LEU 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 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: 3.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118080 restraints weight = 9969.283| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.14 r_work: 0.3297 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8318 Z= 0.130 Angle : 0.559 11.866 11334 Z= 0.281 Chirality : 0.041 0.169 1354 Planarity : 0.005 0.074 1398 Dihedral : 4.950 34.917 1232 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.45 % Allowed : 16.55 % Favored : 81.00 % 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: 1.90 (0.26), residues: 1076 helix: 2.31 (0.20), residues: 644 sheet: -4.44 (0.75), residues: 20 loop : -0.10 (0.31), residues: 412 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 0.019 0.001 TYR A 440 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 2) link_NAG-ASN : angle 2.48915 ( 6) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 5.43674 ( 6) hydrogen bonds : bond 0.03613 ( 507) hydrogen bonds : angle 4.28971 ( 1434) SS BOND : bond 0.00356 ( 8) SS BOND : angle 1.01599 ( 16) covalent geometry : bond 0.00302 ( 8306) covalent geometry : angle 0.54084 (11306) *********************** 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 119 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.920 Fit side-chains REVERT: A 23 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.6354 (tmt170) REVERT: A 195 PHE cc_start: 0.7889 (m-10) cc_final: 0.7679 (m-10) REVERT: A 518 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 23 ARG cc_start: 0.7736 (mtp85) cc_final: 0.6831 (tmt170) REVERT: B 59 THR cc_start: 0.8504 (m) cc_final: 0.8302 (p) outliers start: 21 outliers final: 10 residues processed: 110 average time/residue: 0.8357 time to fit residues: 100.2318 Evaluate side-chains 106 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 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 236 GLN 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 = 0.148513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120470 restraints weight = 9978.591| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.16 r_work: 0.3313 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.122 Angle : 0.550 10.924 11334 Z= 0.279 Chirality : 0.041 0.184 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.880 34.991 1232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.91 % Allowed : 16.20 % Favored : 80.89 % 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: 1.94 (0.26), residues: 1076 helix: 2.34 (0.20), residues: 644 sheet: -4.39 (0.79), residues: 20 loop : -0.08 (0.31), residues: 412 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 0.017 0.001 TYR A 440 ARG 0.001 0.000 ARG B 204 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 2.46205 ( 6) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 4.98351 ( 6) hydrogen bonds : bond 0.03513 ( 507) hydrogen bonds : angle 4.28377 ( 1434) SS BOND : bond 0.00180 ( 8) SS BOND : angle 1.64105 ( 16) covalent geometry : bond 0.00281 ( 8306) covalent geometry : angle 0.53230 (11306) *********************** 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 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.916 Fit side-chains REVERT: A 23 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.6339 (tmt170) REVERT: A 195 PHE cc_start: 0.7883 (m-10) cc_final: 0.7659 (m-10) REVERT: B 23 ARG cc_start: 0.7694 (mtp85) cc_final: 0.6782 (tmt170) REVERT: B 321 TYR cc_start: 0.8403 (m-10) cc_final: 0.7625 (m-10) outliers start: 25 outliers final: 12 residues processed: 111 average time/residue: 0.9119 time to fit residues: 109.7072 Evaluate side-chains 107 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU 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 276 LEU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 470 MET 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: 0.7980 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 0.0870 chunk 77 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.147888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119879 restraints weight = 10137.759| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.19 r_work: 0.3325 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2135 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= 0.115 Angle : 0.544 10.123 11334 Z= 0.278 Chirality : 0.040 0.164 1354 Planarity : 0.005 0.075 1398 Dihedral : 4.761 34.594 1232 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.88 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 17.60 % 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 (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: 1.96 (0.26), residues: 1076 helix: 2.35 (0.20), residues: 646 sheet: -4.38 (0.77), 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 0.014 0.001 PHE B 166 TYR 0.017 0.001 TYR A 440 ARG 0.004 0.000 ARG B 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 2.42539 ( 6) link_BETA1-4 : bond 0.00367 ( 2) link_BETA1-4 : angle 4.65960 ( 6) hydrogen bonds : bond 0.03443 ( 507) hydrogen bonds : angle 4.27708 ( 1434) SS BOND : bond 0.00222 ( 8) SS BOND : angle 1.40380 ( 16) covalent geometry : bond 0.00266 ( 8306) covalent geometry : angle 0.52871 (11306) *********************** 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: 16 poor density : 103 time to evaluate : 0.823 Fit side-chains REVERT: A 23 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.6339 (tmt170) REVERT: A 235 ASN cc_start: 0.8474 (p0) cc_final: 0.8124 (p0) REVERT: B 23 ARG cc_start: 0.7645 (mtp85) cc_final: 0.6771 (tmt170) REVERT: B 321 TYR cc_start: 0.8356 (m-10) cc_final: 0.7593 (m-10) outliers start: 16 outliers final: 7 residues processed: 113 average time/residue: 0.9403 time to fit residues: 114.7804 Evaluate side-chains 103 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 B residue 39 LEU 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 104 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 13 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.147871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119948 restraints weight = 10231.524| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.19 r_work: 0.3325 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8318 Z= 0.117 Angle : 0.542 9.690 11334 Z= 0.276 Chirality : 0.041 0.179 1354 Planarity : 0.005 0.076 1398 Dihedral : 4.708 34.555 1232 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.97 % Favored : 96.84 % Rotamer: Outliers : 1.75 % Allowed : 17.25 % Favored : 81.00 % 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: 2.00 (0.26), residues: 1076 helix: 2.36 (0.20), residues: 646 sheet: -4.41 (0.78), residues: 20 loop : -0.02 (0.32), residues: 410 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 0.015 0.001 PHE B 166 TYR 0.019 0.001 TYR A 440 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 2) link_NAG-ASN : angle 2.48012 ( 6) link_BETA1-4 : bond 0.00291 ( 2) link_BETA1-4 : angle 4.48551 ( 6) hydrogen bonds : bond 0.03425 ( 507) hydrogen bonds : angle 4.26660 ( 1434) SS BOND : bond 0.00314 ( 8) SS BOND : angle 1.26418 ( 16) covalent geometry : bond 0.00271 ( 8306) covalent geometry : angle 0.52749 (11306) *********************** 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 115 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.863 Fit side-chains REVERT: A 23 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.6333 (tmt170) REVERT: A 235 ASN cc_start: 0.8430 (p0) cc_final: 0.8111 (p0) REVERT: A 321 TYR cc_start: 0.8336 (m-10) cc_final: 0.7609 (m-10) REVERT: B 23 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6725 (tmt170) REVERT: B 73 ASP cc_start: 0.8447 (m-30) cc_final: 0.8129 (m-30) REVERT: B 321 TYR cc_start: 0.8393 (m-10) cc_final: 0.7636 (m-10) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.9768 time to fit residues: 113.6302 Evaluate side-chains 108 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 B residue 39 LEU Chi-restraints excluded: chain B residue 276 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 107 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.146434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118227 restraints weight = 10061.328| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.14 r_work: 0.3280 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8318 Z= 0.164 Angle : 0.577 9.027 11334 Z= 0.295 Chirality : 0.042 0.198 1354 Planarity : 0.005 0.074 1398 Dihedral : 4.769 35.407 1232 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.98 % Allowed : 17.25 % 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: 1.94 (0.26), residues: 1076 helix: 2.33 (0.20), residues: 644 sheet: -4.44 (0.76), residues: 20 loop : -0.07 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.018 0.001 PHE B 166 TYR 0.020 0.001 TYR A 440 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 2.74399 ( 6) link_BETA1-4 : bond 0.00427 ( 2) link_BETA1-4 : angle 4.19815 ( 6) hydrogen bonds : bond 0.03676 ( 507) hydrogen bonds : angle 4.31324 ( 1434) SS BOND : bond 0.00599 ( 8) SS BOND : angle 2.43162 ( 16) covalent geometry : bond 0.00395 ( 8306) covalent geometry : angle 0.55905 (11306) ********************** 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: 17 poor density : 95 time to evaluate : 0.949 Fit side-chains REVERT: A 23 ARG cc_start: 0.7357 (mtp-110) cc_final: 0.6356 (tmt170) REVERT: A 235 ASN cc_start: 0.8472 (p0) cc_final: 0.8140 (p0) REVERT: A 468 LEU cc_start: 0.8541 (mm) cc_final: 0.8274 (mt) REVERT: A 518 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8637 (tt) REVERT: B 23 ARG cc_start: 0.7696 (mtp85) cc_final: 0.6815 (tmt170) REVERT: B 356 ILE cc_start: 0.9153 (mm) cc_final: 0.8913 (mt) REVERT: B 468 LEU cc_start: 0.8515 (mm) cc_final: 0.8267 (mt) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.9272 time to fit residues: 104.2767 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 : 0.845 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.147572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119356 restraints weight = 10159.260| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.19 r_work: 0.3298 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8318 Z= 0.150 Angle : 0.587 11.139 11334 Z= 0.300 Chirality : 0.042 0.202 1354 Planarity : 0.005 0.074 1398 Dihedral : 4.828 34.798 1232 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 17.83 % 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: 1.87 (0.26), residues: 1076 helix: 2.29 (0.20), residues: 644 sheet: -4.50 (0.75), residues: 20 loop : -0.12 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.000 HIS B 541 PHE 0.017 0.001 PHE B 166 TYR 0.020 0.001 TYR A 440 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 2) link_NAG-ASN : angle 2.73462 ( 6) link_BETA1-4 : bond 0.00336 ( 2) link_BETA1-4 : angle 4.09319 ( 6) hydrogen bonds : bond 0.03621 ( 507) hydrogen bonds : angle 4.36203 ( 1434) SS BOND : bond 0.00406 ( 8) SS BOND : angle 3.64371 ( 16) covalent geometry : bond 0.00363 ( 8306) covalent geometry : angle 0.55995 (11306) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4970.29 seconds wall clock time: 86 minutes 29.26 seconds (5189.26 seconds total)